Continuity mistake: Lady is put in her bed and the master leaves the kitchen but he goes back in and puts a newspaper on the floor and leaves again but Lady gets out of her bed so the master comes back once more and puts her back in her bed but the newspaper on the floor has vanished.
Continuity mistake: The scene where Col. Hathi inspects his troops, he leans on his stick and it breaks. However, in the next scenes, the stick you see is sometimes broken and sometimes it is still complete.
Continuity mistake: When Dr. Doppler and Jim first observe their ship, Dr. Doppler is right next to Jim when he points it out. When the shot changes to a long shot, they're much farther apart. (00:16:55)
Revealing mistake: In the scene where Rocky and Bullwinkle are walking through the university with Kenan and Kel (right before they come across the anti-moose protest), Kel's right arm passes through Rocky's left several times.
Continuity mistake: When the evil spell takes over the tree in the Forest of Feelings, Brave Heart Lion has his symbol on his belly in the shot as Swift Heart rabbit is coming to the rescue. They don't get their symbols until the end of the movie. (00:41:05)
Continuity mistake: When Tiger and Fievel are doing their musical piece, Tiger wipes off the mirror and they appear the same size. When he lays out in front of the mirror, singing the line "We'll be there to pick each other off the floor", he places his head next to the cage bottom, still laying on the floor between them. In the mirror, however, that cage bottom is not reflected at all. (00:57:30)
Continuity mistake: When they jump in the pool, they drop the guitar. When they jump out their guitar is no longer in the pool.
Continuity mistake: As Flik is just leaving the island to go find the "tough bugs", he's followed by two young male ants. The two young ants look quite different, one being blue and the other more purple. The blue one says "My dad gives you one hour before you come back crying" and the purple one says something to the effect of "My dad says you're gonna die". But after Flik has hit himself on the rock whilst trying to cross the valley, the purple ant says to the blue ant, "Your dad's right, he's gonna die". Wrong ant.
Continuity mistake: When the Were-Rabbit jumps through the stained glass, the right ear is pointing to both dragon wings. But when the Reverend is telling his tale, the glass break is is pushed way over and the hand print is now where the ear print should be. (00:24:55 - 00:28:15)
Plot hole: They go and buy Anne Marie a whole new wardrobe. So, how come in the remainder of the movie she continues to wear her old rags?