The crane that is behind the tree has a rope attached to it, but when Isabella comes the rope disappears.
When the camera pans back as Candace sees the giant cake in her dream sequence, her skirt is red instead of white.
When the "arms" take Perry's hands and feet. The "arms" came from the front of Perry, but in the next shot they've come from behind him.
When Dr. Doofenshmirtz uses his magnet, he opens up the roof of Doofenshmirtz Evil Inc. half way; but when Perry escaped from the building, the roof was completely open.
While Perry was in Doofenshmirtz Evil Inc., a machine breaks a window, we then see the outside of Doofenshmirtz Evil Inc., and there's a hole in the wall, but after, we see the outside of the building again, and there's no hole in the wall.
Ferb states that platypuses are the only mammals to lay eggs. There are in fact 5 mammalian species that lay eggs: platypuses and 4 species of echidna (spiny anteaters).
During the flashback of the roller coaster at the fair, the ride finishes and the ride operator say's "Exit to your left." When the real exit is to the right.