The mine cars commonly used in the 2nd dimension by The Resistance are the same ones seen being used by the animal agents as Agent Perry descends into his lair at the beginning of the movie. The Resistance Headquarters is Agent Pinky's lair, which is why the giant screen is pink and flowery.
During the song "I Found a New Friend and It's Me", the two Doofenshmirtz's appear as several famous duos including Sherlock Holmes and Dr. Watson, Lewis and Clark, Simon and Garfunkel, and the Lone Ranger and Tonto.
Slash's appearance in the credits and his contribution to the soundtrack wasn't Dan Povenmire or Jeff "Swampy" Marsh's idea. Slash had personally reached out to Povenmire and Marsh asking if he come on board to do something for them since he and his kids were fans of the show.
Olivia Olson (Vanessa) was originally in the film. They cut her from it but forgot to remove her from the credits.
Phineas is left-handed, as shown when he plays guitar in "Summer" and uses the baseball bat in Phineas and Ferb: Across the 2nd Dimension.