My theory, and I am sorry if anyone else has thought of it first.
MIND CONTROL.
The Alternate Phineas, Ferb, and Candace(and presumably Isabella, Rover, Buford, and Baljeet)are Resistance members.
However, they were described by Amelia as "cackling" during Robot Riot. In my mind, Doof must have made a mind control machine. Maybe.
What are your thoughts? If you agree, say "Ponypants/Aye", and if you disagree, say "Nay." (Not "Neighhh!!! We are not Agent H, a.k.a. Harrison the Horse, people.)
P.S. I made up the horse agent. Is there one in the show?