Bald Dumbo Rat's canon(Doctor Whooves and Assistant,Lovestruck Derpy,Discord whooves):The Doctor's sometimes gains wings because he's a temporal anomaly. He does not belong in the MLP verse. Cyber toaster's Canon(Shadows of the Lunar Republic, Shattered Stone) The Doctor explains the wings in a line he says when he meets Twilight for the first time."My Dear Twilight Sparkle, I've been in Ponyville as long as you have, pay attention. I even stayed in cloudsdale for a tiff, but those clip-on wings gave me the most horrible rash"