There's been all kinds of gossip, rumour, and innuendo over the years, but not much verifiable concerning rifts between cast and crew.
I think you get that in any well known show with an ensemble cast - Desperate Housewives, Friends, Charmed.
A lot of the BTVS gossip spawned out of SMG as diva stories. It was a popular rumor to spread. Stuff like SMG had one of her stunt woman fired, because she said SMG didn't do her own stunts, or Seth Green didn't like her, or everyone was happy when she couldn't make the Buffy wind-up party. But then you hear the actual people talk about SMG in interviews, and they have nothing but glowing reports as to what it's like to work with her.
There's been a few rumors concerning rifts between Joss Whedon and actors Glen Quin and Charisma Carpenter. Again all we know for sure there is it's gossip.
The only Alyson Hannigan one I know of concerns a comment Hannigan supposedly made insinuating she wasn't happy with SMG not giving the rest of the cast some warning she wasn't continuing after Season 7.
I don't know the Emma one, but she wouldn't renew her contract during S 7 before the cancellation, so I imagine somewhere there was a rumor saying it was because of SMG. That was a popular kind of thing to say in gossipy circles.