Revealing mistake: The film was rushed to theaters, leaving a few mistakes which Universal fixed. In the original cut, toward the end, Judi Dench's human hand is visible, complete with her wedding ring. This was fixed for the re-release.
Continuity mistake: When Ash and friends are entering the wharf, there are two people that change between shot. There is also a person who goes from having his right hand in his lap to having it scratching his head. (00:23:06)
Continuity mistake: When Buzz is first put on the prize board at the carnival game, Ducky and Bunny are hanging further down and Ducky is pretty much level with Buzz. Later on, they are hanging higher up and Ducky struggles to reach Buzz when trying to kick him. (00:34:22 - 00:43:00)
Continuity mistake: En route from the front door of Wayne's mansion to the table in the Batcave, the pile of pizza boxes in Alfred and then in Mike's hands continues to change in size and number: at first the pizza girl delivers 11 boxes, Mike slams on the table just 8, but he brought down the stairs twice that amount (without counting through freeze-frame the precise numbers, it's simply obvious at first glance that the pile is bigger in some shots and the pizzas themselves are pictured of inconsistent size).
Other mistake: When the characters go to the Himalayas, the whole time, like for 20 mins, including the confrontation scene, they are all wearing casual, short-sleeved shirts. You can see Mr. Burnish's henchmen wearing winter clothing, while the main characters don't freeze to death. They only start getting cold after a long time.
Continuity mistake: Bruce and Selina sneak away from the party while Bruce's neglected childhood friend fetches the drink. The bottles on the shelves behind the counter change between shots when he goes "Seriously? Both of them?" It's like a portion of the leftmost shelf has been sliced off for the close-up. (00:05:00)
Continuity mistake: At the start of the film, Eggman is chasing Sonic through the streets and there is a shot of the city skyline down a street behind Sonic as he makes a turn. The camera then cuts to inside Eggman's ship to a close up him with the city skyline still behind him, only now it's different buildings behind Eggman. (00:01:00)