Legitimate question, how many civil wars has this fandom went through?
Legitimate answer, it kind of depends on what you consider the threshold for a “civil war”. There have been any number of fan fights over the years, regarding everything from big, show changing events down to relatively minor arguments, but not everyone is going to agree on whether it qualifies. Also applicable, separating out particular fights from larger ones can be difficult. Case and point, issues regarding the quality of season 3 could possibly be considered a bit of a civil war, but it also exists as a subset of the larger argument over the Equestria Girls franchise and the (repeatedly denied) rumor that the season suffered because of work on that first movie.
But on a less serious note, this is the internet. Civil war is so common here, even an amphetamine abusing Ken Burns on his 6th espresso of the day couldn’t keep up with it all.
Still, if you’re looking for the big ones, Derpy’s voice change, Season 3/Equestria Girls, Twilight becoming an alicorn, and Starlight Glimmer are the ones that stand out best in my mind.