In the junkyard when Vern is talking about the "goocher" he mentions Weed Hill in Durham. This is a reference to Durham, Maine as Durham, Oregon was not incorporated until 1966, seven years after the timeline of the movie.
When the boys set out on their Journey, there is a shot that shows them walking on the tracks and singing "The Ballad of Paladin" which is a song originally written by Johnny Western, Richard Boone and Sam Wolfe and released in June of 1962. However, the movie was set in pre-1960's Oregon. The boys obviously know the lyrics, which would lead one to believe it was a recent hit on radio. But the song hadn't even been released per the setting of the film. However, the song was used at the end of every TV episode of "Have Gun - Will Travel" from 1959 to 1963 so the boys learned the song from watching the TV series.
When Vern is first coming into the tree house and is coming through the trap door he is clearly heard saying "You guys are never gonna believe this...", but his mouth is saying the previous lines "Oh, man, oh, man".
Teddy's left ear (which his father almost burned off) in the treehouse scene is very clearly burned. Throughout the movie, however, it varies in how it looks, in the train tracks scene it looks perfectly normal.
All four guys are in the junk-yard and they are all about to toss their coins to see who goes to get the food. When Teddy throws his coin in the air he is wearing no dog tag necklace but when he catches the coin he is suddenly wearing the dog tag necklace.
When the boys are seen walking into the leech pond, they all fall in. We see Vern and Teddy go into the water, and when they come back up to surface, we can see Chris and Gordie on the surface already on the right side of the screen. However, in the very next shot, Gordie and Chris come to surface again.
Gordie's hair constantly changes throughout the film from floppy to gelled, i.e. in the scene on the trestle over the water he yells, "Train!" and his hair appears to be quite dry, without a parting. In the next short scene around the campfire, it looks perfectly combed and gelled. He can not have borrowed Vern's comb, since Vern lost it on the train bridge.
When the boys are crossing the bridge, and Gordie is trying to help Vern to his feet there is a very brief cutaway showing that the oncoming train is only the engine and one car. The previous shot, and the later one once it passes, all show it to have several cars.
When Gordie shoots the garbage cans and runs off, he's still running when they get around the corner and he's not holding the gun anymore. He wouldn't have dropped it because it's in later scenes, and he didn't have enough time to put it in his backpack or give it to Chris because they were trying to get far away from the back of the diner.
In the swamp, the four boys get completely wet, then they strip down to their underwear to remove all the leeches, and Gordie faints after a leech is found on his nuts. The next scene when the boys are putting their clothes back on, they and their clothes and sleeping bags are completely dry.
When we're first introduced to Teddy Duchamp in the Tree house. We see his badly burnt ear but also on the same side of his face he has a big mole at the side of his nose. When they set out on their adventure, it's disappeared and never seen again all movie.
When the boys get dunked in the swamp, Teddy takes his glasses off, but then while they're thrashing around in the water, both hands are clearly empty. Then, when they get out, he has his glasses in his hand again.
At the Leech pond when the boys are dressed again, they and their clothing appear as they were before they entered it, dry, clean and tidy. Their clothing would have been saturated and, therefore, taken quite a time to dry as well as being dirty from the muddy water. Their hair is immaculate and well groomed. Someone in continuity failed to notice Vern was the only boy who had a comb, which he lost at the trestle bridge.
When Gordie is telling the story - when they are sitting round the campfire - Bob Cormier moves back and is squashed up against Principal Wiggins just before David Hogan (Lardass) barfs on Billy, but in the next shot he is not.
All four boys are completely submerged in water when they fall into the leech pond, soaking their hair. When Teddy and Vern are wrestling with Chris, there is a shot of Gordie leaving with completely dry hair. In the next shot, Gordie's hair is all wet again.
Teddy is not carrying his bedroll as the boys leave the junkyard, because Chris actually grabs it as he drags the enraged Teddy away, and continues to carry it while comforting him. Gordie, in turn, is carrying Chris' bedroll; Gordie's own sleeping bag is evidently inside his backpack.
The train tracks the boys are traveling are obviously active - trains pass through multiple times during the boys' journey. In some shots the top of the rails are bright and shiny, which is how they should appear in active lines where trains continually wear and polish them. However in some scenes the tracks are clearly from unused lines, as the tops of the rails are rust colored like the sides. A good example are the rails when the song "Lollypop" plays - that scene was shot on a seldom used or totally inactive stretch of track. Since they are supposed to be walking on the same line the entire time, the rails should always be shiny.
During the "barf-o-rama" scene, the two twin brothers barf on each other. As the second brother barfs, the other brother turns his head and you can see the white tubing of the barf mechanism on or around his left ear.
In the tree house scene, right after Chris says to Teddy, "come on man deal", Teddy blows smoke from his cigarette while laughing at the same time. As he's doing this, we can clearly see a film camera right next to Chris' head in the reflection of Teddy's eyeglasses.
Like many of Stephen King's stories, the original story takes place in Maine. Although relocated to Oregon, the movie has several holdovers to the original location, such as the reference to picking wild blueberries. Also, the junk man teases Teddy by telling him is father will be "sent to Togus" (which he mispronounces as Tau-gas instead of Tow-gus). Togus, Maine has a large veteran's hospital, which would be the logical place (in Maine), for Teddy's dad to get treatment.
Near the beginning of the movie, Vern is described as burying then losing a quart jar of pennies "at the beginning of the school year," and searching for it for the last nine months. But the story takes place Labor Day weekend, so that description is inaccurate unless Castle Rock's school year coincides with the calendar year. The story may have originally been set on Memorial Day, for which the time frame would have been accurate.
Ben E. King's "Stand By Me", which the film derives its title from and uses as its theme song, was not recorded until 1961. However, it is non-diegetic (not heard by the characters), and it is also first heard when Gordie is an adult in the film's opening scene, which would be well past 1961.
In the "barf-o-rama" scene, all the actors vomit up blueberries, just like Lard-Ass and the other contestants in the pie-eat. Nobody in the audience (at least from what is shown) ate any blueberries. However, this is a silly story which Gordie is imagining, and he hasn't got everything right in his mind.
When Gordie goes into Denny's room looking for his canteen, a Michigan State pennant is displayed on the wall. Although the school was officially named "Michigan State University" until 1964, in 1954 the name was changed from Michigan State College of Agriculture and Applied Science (MSC) to Michigan State University of Agriculture and Applied Science (MSU) in 1954. All that happened in 1964 is that " Agriculture and Applied Science" was dropped from the official name. Thus, the pennant would be correct for the time period, in the late 50's, when the school was referred to as MSU/Michigan State University.
In the car race, a log truck is rapidly approaching Ace in the oncoming lane. Four shots of the log truck are shown as it gets closer. The first three shots show the road with no visible roads or driveways connecting. Then on the forth shot, a road/driveway (that was never there) suddenly appears, allowing the log truck to veer off the road at the last second.
In the train scene, River Phoenix' voice has suddenly changed and he looks older. This scene was obviously shot last, and he has started going through puberty. But in terms of movie time, he has gone through puberty in two days.
The goof items below may give away important plot points.
At the showdown with Ace near the end, Gordie fires one shot into the air from the 1911 .45 pistol. Afterwards, in order to add effect to his assertion that he would shoot Ace, he cocks the pistol. However, the pistol would already be cocked after firing the first round as the 1911 is a single-action automatic and firing causes the slide to cycle back and forth, cocking the gun to prepare it to fire the next round in the process. It's not impossible that he would de-cock the gun after firing the first round, but it's highly unlikely and certainly nothing shown in the film suggests he did this.
The narrator does not save his work before appearing to shut off his word processor, but that's okay, because in fact he only switches off the monitor, leaving the machine running and his work intact. Also, the shot of the narrator writing has him seated at his desk; when he turns off the word processor, he is standing, studying his work. It is reasonable to presume that a brief moment went by between the shots, and he could easily have saved the work then.
When the boys find Ray Brower's body, the train tracks are fake ones laid out on a trail close to the river. The trees are too close to the tracks, either from the sides or the canopy, for a real train to pass by recently and hit the boy to kill him.