Hopper was killed by the red bird's baby birds. Princess Atta is now the queen and it seems she likes Flik. The circus bugs leave Ant Island and Heimlich (the caterpillar) becomes a butterfly.
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.
Hopper: If I didn't promise my mother on her deathbed that I wouldn't kill you, I'd kill you!
Mulch: You know, no one appreciates that more than I do.