Factual error: The size of the shadow of an object depends upon its distance from the light source, not the surface it falls upon. Lifting the cutout of the bird a few inches closer to the sun as they do would make absolutely no difference to the size of its shadow, yet it quadruples in size.
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: In the opening sequence where the ants are loading the food onto the leaf, they show a panoramic shot of the scene, and you can see the queen and the princess standing under the shade near the center. But, in the very next shot, the ants are still hauling the food, and the royal family is no longer there. (00:01:56)
Continuity mistake: When Gypsy the moth spreads her wings throughout the movie, the number of yellow spots on her wings change.