I had the same problem with my rabbits, the female was not only aggressive to the male, but she would not let me clean out the cage, she was nasty to him pulling out lumps of fur and biting his back. There seemed to be a pattern to her moods, she pulled out her fur to make a nest as if she were having babies. I kept a close eye on them but never separated them. In time she settled down. I am still a little unsure of cleaning her cage when she is in it. The vet advised maybe having her spade would cure the problem, but I never did and my rabbits are the best of friends now. They follow each other around my garden. She is still rather bossy and insists on him cleaning her ears but she is not at all agressive to him. This stopped after about six months. I think it is just hormones, like most women.