Tom Sawyer sneaking back into his house after returning from the graveyard is wearing different clothes (orange shirt and brown pants).
When Tom and Becky are lost in the cave, Tom has her wait while he looks for a way out. He comes upon Injun Joe in the cave, who chases him. Tom had shoes on when he got to the cave, he has them on when Joe starts chasing him, then in one shot (1:08:58) as he is still being chased, Tom is barefoot. In the next shot he once again is wearing shoes.
Although the book is set during the early 1850s, there is a picture of President John Tyler (1841-1845) in the school/courthouse.
When Tom wakes up the first morning after he and Huck reach Jackson Island, he sees a fox crossing a wide, fast flowing stream with a rocky bottom. The narrator has described Jackson Island as an "uninhabited thin and woodsy piece of free floating land." The island certainly wouldn't be big enough to support such a stream and the clear water certainly wouldn't be coming from the muddy Mississippi. The shot is stock or second unit footage.
Tom gives Muff a package with "a little bit of bacon, some bread, and a pack of cigarettes." Although the movie presumably takes place in the 1840s or 1850s, cigarettes could not be bought pre-rolled until the 1880s and were not put into packs until 1915. In addition, American males either chewed tobacco or smoked cigars since cigarettes were considered effeminate.
In the novel "Adventures of Tom Sawyer", when Injun Joe and his partner dig up the coins in the haunted house, Tom hears Joe say he will bury the coins at den "number two", but Joe does not say this in the movie. Consequently, when Tom is lost in the cavern with Becky, sees Injun Joe and says "So this is number two" (at 1:08:27), there is a disconnect: viewers unfamiliar with the story fail to make sense of this line. When Tom returns with Huck and finds a Roman numeral II on the cave wall (at 1:13:30), there is a similar disconnect.
Ben Rogers says he will give Tom his switchblade knife for the privilege of whitewashing part of the fence (at 0:19:50). But the knife Tom opens (at 0:20:34) is not a switchblade knife.
Aunt Polly tells Tom "You will paint the picket fence ... picket by picket." However, the fence is not a picket fence.
Someone who is trying to act as cool as Huckleberry Finn is trying to act wouldn't let Tom Sawyer call him "Hucky"; adding the suffix -y or -ie to a name is a term of endearment for a young child, not a cool dude.