In one shot during the aftermath of Marty's "shootout" with Tannen, a modern California state flag can be seen hanging from one of the buildings. This design was not developed until 1911, the original having been destroyed in the Great San Francisco Earthquake of 1906.
In 1885 the train engineer is wearing a traditional striped hat. This type of hat was invented by George Kromer in 1906. In 1885, railroad men wore the same type of hats as any other person engaged in physical labor.
When Doc Brown demonstrates the plan on the model of the railroad, the words POINT OF NO RETURN are written on a book. That book is The Young and Field Literary Reader: Book 4, which was originally published in 1910.
Towards the end of the film, Mad Dog Tannen is holding Doc Brown hostage trying to lure Marty out into the street for a duel. He tells Marty that if he doesn't face him now, he will shoot Doc Brown. When Marty doesn't come out, Tannen pulls his single action Colt pistol and points it at Doc's head. When he does this we can hear the distinctive clicking sound of the hammer being cocked as he's raising the gun, but his thumb never actually touches the hammer at any point when he draws his pistol.
The 1955 Doc states that his future self might have landed in the Dark Ages and been burned as a heretic. However, it's shown throughout the trilogy that the DeLorean can only travel through time and not space, so the 1985 Doc would have landed in California in the Dark Ages (circa 1000-1500 A.D.), at which time Christianity was unknown to the locals.
When Doc Brown and Clara are talking about Jules Verne's 20,000 Leagues under the Sea, Clara states that the book was written 10 years before. In fact, 20,000 Leagues under the Sea was published in 1870, 15 years before 1885, when the movie takes place.
When Doc says "I put gas in the tank", the shadow of the building stretches only to a few feet past the DeLorean. But two lines later, when Marty says "Hoverboard" and gets it, the shadow has stretched all the way to Doc's 1955 car.
After the scene in the saloon with Mad Dog and Marty, Mad Dog has a soiled shirt due to the spittoon. In the following scene when Mad Dog and his cronies are chasing Marty on their horses, Mad Dog has a clean shirt.
When Clara is on the train to leave town, she pulls a cord to trigger an emergency stop. Her hands are clad in dark brown leather gloves. However, right after she gets off the train and begins running, her hands are not gloved. She is then seen wearing these same gloves throughout the remainder of the film.
The shadows during the showdown: the camera angle from low down behind Marty shows him in full sunlight from the front, in other shots the sun is clearly throwing shadows at angles to Marty. After he's being shot, Marty ends up well into the shadows of houses.
The telescope changes position in Emmett's hands while he's talking to Clara in the barn. This is evident from the position of the adjusting wheels on the side of the telescope. Their position keeps changing showing the telescope is being rotated, but throughout the conversation, Emmett never moves his hands in that manner.
During the scene where Doc places the old white wall tires from 1955 on the front of the train as padding against the bumper of the DeLorean, he places the front tire with the white wall facing outward towards the bumper. Later as the train careens off of the uncompleted bridge, the tires are visible and none are white wall tires.
When Tannen is shooting at Marty in the saloon and making him dance, the position of the spittoon changes. Also the board he kicks only appears loose and out of shape just as he's about to stomp on it - prior to that it was a solid, smooth wooden floor.
Marty wears his red and white colored Nike sneakers throughout the film; but when Marty and Doc Brown are in the mine in 1955 to find the DeLorean, he is wearing black and white Converse Taylor's or "Chucks"
When Buford Tannen starts to hang Marty at the new courthouse, we see 'Mad Dog' whip one loop of rope around Marty's neck before he pulls the rope tight to tie it to the hook. After Marty is pulled up into the air we see a closeup of him with his fingers inserted into at least three loops of rope around his neck.
Doc rides bareback to tell Clara goodbye (his unsaddled horse is hitched at the saloon the next morning). Likewise, Marty rides bareback to find Doc that morning. Yet both jump on saddled horses after the gunfight to catch the train.
When Marty is facing Mad Dog in the street, Tannen tells Marty to draw and Marty says "NO". There is a close up shot of Sheamus and Chester the bartender standing near each other with a post in between them, and 4 or 5 cowboys standing immediately behind them. When the camera cuts to shot of Doc Brown and Tannen's henchmen, you can see Sheamus and Chester behind them on the porch of the saloon, but now they are standing nowhere near the post and about 10 feet apart and there are no longer any cowboys behind them. This happens a few times during this scene.
At the beginning, while Doc is dictating into his tape recorder, Copernicus is on the right side of the couch. As Marty says, "Hey Doc," Doc turns around and screams. As he screams the camera cuts to a view of Marty, and Copernicus is on the left side of the couch. The next instant as Doc is falling backwards, Copernicus is seen on the right side of the couch again.
When Marty is running away from Buford Tannen and his gang after their first encounter at the saloon, a crewmember in blue shorts and a white t-shirt is running alongside a camera on the left side of the screen.
Towards the end When Marty questions the people in the bar by saying," What...what if I don't go out there?" On Marty's right, a film light on a stand is clearly visible sitting in front of the window.
When Marty is in the cave with the bear the scene looking out of the cave shows the desert going on for miles. But when he runs out of the cave there is a little hill about 300 feet out, with the cliff just beyond it.
When Marty first arrives in 1885, he's driving (and running) around red brush-covered desert terrain with monolithic geography on the horizon. As he runs over a hill away from a bear, he stumbles down a hillside and crashed into Seamus McFly's fence. As the camera pans up to Seamus, the countryside is lush and green, with rolling hills.
The locomotive, Central Pacific no. 131, in the film featured a Ten-Wheeler arrangement of 4-6-0. While the Central Pacific did have such locomotives in 1885, the number 131 actually belonged to an American type, which had a 4-4-0 wheel arrangement.
The complex logic, and conflicting theories, of time travel have resulted in a great many potential plot holes, especially when the movie is viewed in the context of the whole trilogy. But time travel movies are like that.
George McFly's great-grandmother looks just like his wife. It may just be coincidence that Maggie and Lorraine look alike, implying that McFly men have always been attracted to women who look like her. Or this could be an allusion to the notion that in small communities people often choose their own distant (or close) cousins as mates.
At the end of Back to the Future Part II (1989), Marty sets the hover board on the ground while burning the book and doesn't pick it up at any point and doesn't have it in his possession when he gets the 1955 Doc to help him get to 1885, but it is still seen in the car when he goes back to 1885, even though it was apparently left at the sign. Marty does in fact have it in Doc's house at the beginning of the movie, and it's implied that a few hours have passed between films, so Marty would have had time to run to the sign, get the hoverboard back, and bring it to Doc's house.
For Marty to avoid crashing into a tree that once existed in the past, Doc felt it was safe to send Marty back to 1885 at a drive-in as he says, "this was all wide open space". Some viewers have questioned how Doc could know this information. However, it is entirely possible that he looked it up at the library before leaving (also, he could have gone back before or while repairing the DeLorean, which would take at least a couple of days anyway, even assuming he already had everything he needed, which is unlikely) or that he, or a friend of his, had a map of the general Hill Valley area as it was in late 1885 in his possession.
Marty is heard cocking the pistol. The Colt Peacemaker is a single action pistol, which means the hammer must be cocked back before each shot. Double action revolvers (which had not been invented in 1885) can be fired by only pulling the trigger, or first cocking the hammer back.
When Marty and Doc look at the Delorean's damage. Doc notes that the car needs parts and says, Where are we going to find gas/parts for the Delorean at this time? If they went back to the cave where Doc put the Delorean for Marty to find, he could have gotten the parts from there. But if they took parts from the hidden Delorean, they would create a paradox because if they damaged the past Delorean then the Delorean that Marty used would be damaged to the point where the "1955" Doc Brown could not fix it, which would mean that Marty could not go to 1885 to rescue the "1985" Doc Brown and damage the Delorean that is in the cave.
As the train carrying Clara is leaving the station, the rail underneath the locomotive drive wheels appears to be wet, causing the wheels to slip. However the rail could have been wet from the boiler's water tank. Or it could be oil on the rails, since the locomotive engineer puts oil on the moving parts of the wheels and drive mechanisms before leaving the station.
On the morning that Marty is suppose to have his shootout with Mad Dog, an automated machine in Doc Brown's shop makes breakfast. One part of the machine cracks some eggs and slides the frying pan over to an open fire. But as this happens, the eggs are pushed over too and you can see that some of the egg whites are already cooking, suggesting that the pan is already hot.
When Marty moves his fork and knife to the plate of rabbit next to him, he doesn't actually take a piece, even though he acts like he has one and brings it back to his plate. When the camera switches to Shamus, then back to Marty, Marty suddenly has a bite of rabbit on his fork that he puts in his mouth, but his plate is still devoid of any larger piece he would've pulled it from.
In the beginning of the film when Doc wakes up and tries to remember what happened after the DeLorian time traveled, Marty scares him and he falls back onto his organ. This organ is actually a pump organ and requires air to fill via pedals to make a sound. Also the sound played is of a pipe organ. Pump organs make a more airy, reed type sound not the sound of a pipe.
When Doc and Marty hold up the train and one of the engineers disconnects from the train from the cars, Doc is pointing the guns at the engineers and they have their hands up. Then the engineer puts his down while Doc is pointing the gun at him and then puts them back up when Doc turns away with the gun.
When the final log blows in the locomotive, a close-up of the boiler shows rivets popping out and jets of water coming out of the holes. In all subsequent shots of the locomotive, all the rivets are still in place.
Right after the third log blows, in a long shot of the train from the side, you can see Clara's feet dangling from the train briefly, even though in the previous and subsequent shots, she is hanging upside down.
When the train in 1985 is approaching the car, the shadow of the engine on the solid fence along the side of the tracks shows the engine is by itself but a couple of scenes later it is a full length freight train.
As Clara's wagon goes over the cliff it rolls over sideways spilling some of the contents, but in the next shot the wagon is going over straight forward with the contents still in it until it almost hits the bottom.
When Doc and Marty are first out at the unfinished trestle there is nothing on the trestle tracks but later when the engine is on the unfinished trestle after pushing the time machine, there is a cow catcher-like barrier at the very end of the trestle, which the engine hits. But when a front view of the falling engine is shown there is nothing on the front of the engine's cow catcher.
The headrest on the drivers side of Marty's pickup truck is missing when Biff opens the door for him toward the end of the movie, however when Marty is stopped at the intersection preparing to race Needles the headrest has reappeared.
As the DeLorean time machine is being pushed by the locomotive, it smashes through a sign indicating the end of the track in 1/4 mile. At that point, the DeLorean's digital speedometer reads 80 mph. At this speed, the vehicles would reach the end of the track in about 11 seconds.
Towards the end of the movie when the train is bearing down full speed towards the time machine the front of the engine has only the top headlight on but under federal railroad administration rules ditch lights (the lights on the catwalk on the front and rear of the engine) are required to be both present and on.
At the end, when the Delorean is being destroyed by the train, the time machine breaks into thousands of pieces, and these pieces nearly stay where the car stood when it was hit. A single train would never be able to smash a whole car like this and would rather drag the car until they would both stop. In BTTF I, Doc even says that the Delorean is made of steel.
During the film, Doc urges Marty to destroy the time machine once they return to 1985, as time traveling has caused enough trouble for them already (such as almost preventing George and Lorraine from meeting, Biff getting rich with the almanac, and Doc being sent to 1885). By the end, Doc seems to have forgotten this and made a habit of time traveling with his family. This is a running gag--Doc can't resist the temptations of time travel for long.
In Back to the Future Part II (1989), it is mentioned that Marty's life was partially ruined by a car accident in which he raced his rival, Needles, and crashed into a Rolls Royce, whose driver sued Marty in court and therefore ruined his life. Back to the Future Part III (1990), however, depicts the (avoided) accident in a completely different light: during the race, the Rolls Royce speeds through a STOP sign onto the main road, thus getting in Marty's way and causing the crash. While the courts would normally find someone who drove through a stop sign to be at fault, it can be assumed that the driver of a Rolls Royce is wealthy (certainly more so than Marty) and would be able to afford lawyers who could influence the court in their favor.
When the diesel locomotive, Sierra County Railroad S-6 #11, hits the DeLorean in 1985, the engineer doesn't stop the train, nor do any motorists seem to notice the accident (several are seen staring incredulously at the DeLorean as it passes by a nearby railroad crossing less than a minute before the DeLorean's destruction). Furthermore, Marty and Jennifer return to the scene roughly an hour later, yet no police/fire/EMS have apparently been alerted to what would have been a very serious accident.
In the final scene of the movie, the child playing Vern Brown makes a beckoning gesture with his hand, then points toward his crotch. It's with his right hand, just visible past Doc Brown. The boy was mimicking the unit director, who was directing the camera to pan then zoom.
The Boiler Temperature gauge in the time machine is not connected to the Locomotive. We can see this as the Locomotive approaches the time machine to begin pushing it. There should have been a hose running between the gauge and the boiler.
When Marty arrives back in 1985 and sees the freight train hurtling towards the DeLorean, the shadow of the approaching train initially reveals that only one locomotive is used for the approaching shots; the second locomotive and freight cars are not attached until right when the train smashes the DeLorean (and the shadows of the freight cars become visible at this point.)