The funnel above Candace in the dining room does not appear until she mentions it.
In the final shot, when the characters are raising their fists, Isabella suddenly disappears and then reappears out of nowhere. Also in the wide shot Baljeet on the right side of Ferb but in the close up he's on the left side of Phineas.
When Phineas sings "When you blew up all those aliens", the Fireside Girl sitting below Adyson Sweetwater has blonde hair. In the next shot, her hair is black.
When Baljeet comes out with the easel, he is holding onto the side of it. Suddenly, in the next shot, his hand jumps down to holding a corner of the paper on the easel.
When Baljeet, Isabella, and Buford are first seen driving the golf cart, Baljeet is holding a rake. However, two shots later, when the Wilhelm Scream is heard, Baljeet is no longer holding a rake. It reappears several shots later.
During "Adulting", when Isabella shows Doof her patches, their lip sync is slightly off.
Candice is chosen by the aliens because of her ability to exhale "Remarkalonium", aka carbon dioxide. Super Super Big Doctor completely ignores the fact that Phineas, Ferb, and the other humans who come to the planet also have this "ability".
Super Super Big Doctor keeps referring to "Remarkalonium" as an element. Later, it is revealed that "Remarkalonium" is actually carbon dioxide, which is a compound, not an element.