It's not always a male/female thing either. It's just plain a hormonal thing I think. We had Pooky & Bear neutered at 5 1/2 months old (which is about 1 1/2 months earlier than the vet prefers) because they started getting aggressive with each other and the other cats. Even though both male and brothers to boot, hormones seem to override relationship.

I think once things are healed up from the neuter you should start seeing your kittes learning to get along again. If not consult your vet in case there is something else going on.