It's not so much communities where hate was constantly spewed, but a kind of more generalized... bad feeling. Posts about how one series was better/deeper/whatever than the other, passive-aggressive comments, stuff like that. It was going around, though, and not super nice on either side.
I'm definitely glad you didn't have to go through that, and had a positive fandom experience, though :)
I generally do have fond memories of the fma fandom, though it was kind of wanky, looking back. I guess most large fandoms are, though.