In "Let's Bounce" when Suzie is shown under the table removing the wrench from Candace's sock, she is not shown to be wearing underwear. However, when the action returns to The Flynn-Fletchers from Doof and Perry, Suzie is wearing white panties.
In "Bully Bromance Break Up" when Buford finds Baljeet in the ice chalet with his GPS, it is the right side button on Baljeet's overalls that blinks red, but when Buford pulls the GPS button off in the end, he pulls off the left side button.
In 'Lets Bounce' Linda tells Candace to get 10 plates for brunch with the Johnsons family but there's 4 in the Johnsons and 5 in the Flynn-Fletcher family so it would only be 9 plates needed.
The people of Drusselstein argue over whether the goats powering the great shaft should go clockwise or counter-clockwise. Phineas and Ferb solve the problem by having the shaft turn both directions but when the goats are shown, both groups of goats are moving clockwise. The wheel that the second set is attached to, however, is turning counter-clockwise.