Visible crew/equipment: When Fred is chucked on the table and says, "Watch the silk." you can see that its Fred's stunt double as he's a lot fatter and his hair is obviously a wig also he does a really good job of covering his face so the audience can't see hes a stunt man.
Audio problem: After Johnny escapes into the city, Ben returns home and starts to shout at Fred for letting him get out. Watch Freds mouth closely as he replies, some of the words he says back to Ben have been removed. Judging by his mouth movements, they appear to be swear words he is saying, and as the film is rated as PG, they were probably removed so they would not cause offence.
Audio problem: Quite a few scenes in the film appear to have been dubbed over. Most of them are at the start after Ben and Fred have to keep Johnny 5 indoors. The mouth movements don't seem to match up with what is being said. If you look at the mouth's of the actors, there appears to be quite a few strong swearwords in the film, which were probably removed because it's a kids film.
Factual error: When Johnny shoots the taxi with some kind of cable and pulls it backwards, the rear tires are shown to be spinning in an attempt to move. The taxi is a Chrysler K-car which is front wheel drive.
Deliberate mistake: When Johnny Five is assembling the first toy robot, he takes a screwdriver to the neck and body of the robot toy, even though there are quite obviously no screws there for him to tighten.
Revealing mistake: After Johnny Five falls out the window and whips out his hang-glider, as he turns right-side up and soars past the buildings, you can see that his body is transparent (an artifact of the optical matting process used).
Revealing mistake: When Johnny Five is showing off his remote-control transmitter and begins making the toy robots dance, you can see the cables leading from the robots into the table, and the little plastic mounts underneath each robot toy.