This explains a lot. My guess is she had a botched eye surgery that made her eyes like that.
Actually I think it’s more that she always had the derped eyes, it’s just here she happened to get into an accident where she injured her eyes.
In case you don’t believe me, remember this scene?
Derped since birth.
wasn’t that the episode that took place in the present though and for some reason she was still there?
No, that gif was from a flashback sequence in “Pinkie Pride” when Cheese Sandwich gives his backstory (You can also see a younger Lyra and Bon Bon, Cheerilee, and Minuette).
(Filly Derpy appears at 0:33 and 0:42 specifically)
I am Silver Tongue, I am an artist. I have many characters and you can check out my art in the art tag. I occasionally practice witchcraft though I don't do anything too complicated. I am girl 2 and don't know what else to put here.