Revealing mistake: During the sequence with the Native Americans chasing the Delorean in the beginning, in one shot looking up at the sky you can see contrails from a plane, obviously not around in 1885. (00:19:25)
Continuity mistake: Kevin sits down with a meal before the Wet Bandits arrive at the house consisting of macaroni and cheese on a plate. When Harry eventually makes it to the dining room, he is pelted with feathers. Look at the table to the left. A three part microwave meal still in its white plastic container now sits on the plate.
Visible crew/equipment: When Splinter throws Shredder over the wall, Splinter's puppeteer is visible. (Full screen only).
Continuity mistake: When Tracy is tied up in the basement, the rope around his body changes styles between shots.
Continuity mistake: When McLeach is using Cody to fish for crocodiles, the hook fastened to the rope around Cody's waist can be seen facing different directions in various shots. (01:06:45 - 01:09:35)
Continuity mistake: The telephone on Scrooge's desk briefly disappears after his maid delivers an invitation to the archaeological society ball. (00:19:05)