In the scene when Gordie and Chris are discussing the stolen milk money Chris uses the term "douchebag." The movie takes place in 1959, however the slang version of this term did not originate until the 1960's, with its more prominent usage beginning around 1967.
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.
In the scene where the guys are cutting "cobra" into their arms, a VW Beetle can seen among the old cars. The style of tail lights on the car show it to be anywhere from a '62 to '66 model year, while the movie takes place in 1959.
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".
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.
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.
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.
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.
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.
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 confronted by Ace's gang, Gordie shoots the pistol into the air, and then points it at Ace and pulls back the hammer. The pistol is a Colt 1911 and is an automatic, which means the hammer would have already been cocked after the first shot.
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.
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.
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.
In the first scene on the railroad tracks, there is a turn-out switch with no closure rails beyond the points. It is clearly not an abandoned spur, and any train using these tracks would be derailed at this point every time.
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.
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.
In the scene where 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's 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.