Apparently so. I don't quite remember the story, but I think it went something like this; back when she first made a proper speaking appearance, certain groups objected to the character and felt she was a stereotype of mental handicaps or disabilities, like Autism. They reanimated and revoiced the character as well as dropping Rainbow Dash calling her by her fan-bestowed name "Derpy" for reruns and official home media/online releases of that episode. It was never the intent to cause a ruckus or stereotype a real thing that people have, but while I can't exactly blame them for seeing her as such, I still feel that some people just read too close between the lines. Of course, that was back in 2011, when the show was still new. Nowadays, we see her coming up again under the name "Muffins", even accompanying Doctor Whooves(aka Time Turner) in their plotline of the fanservice-stuffed season 5 episode "Slice of Life".