Help!

Hello! Let me start from the beginning I have two bunnies both different breeds. The first one that was brought to household was Claire, a lion head. She was brought as a baby bun and took claim over her territory right away when her sister Cleo, a Holland lop, was introduced to her a few days later. Their friendship started with aggression, Claire targeting Cleo, but soon let to them being the best of cuddle buddies. They have spend the last 3 months with a giant pen to constantly roam, cuddle, eat, and sleep. Since their first meeting there has been almost zero signs of aggression towards the bun buns. Unfortunately this morning we woke up to Cleo with two bite/cut marks on her ear, blood spots on the floor, and Claire’s fur everywhere . We don’t know whether there could be a possible rat attack because we have seen little evidences of a possible rat in the area they roam, or if the rabbits suddenly turned on each other. We brought them out of their pen to be observed and they were cuddling and being their usual selves until Claire, the obvious, alpha started to chase Cleo around. They are currently separated as seen in the phot but do have moments when they try to reach each other. Should I be worried that their relationship could become aggressive? Should I keep them separate or is this something that is “normal”? We believe my buns are both girls and around around 3-4 months. Neither are spayed.

Keep them separate for now. And be careful: they can hurt each other pretty seriously even through the openings of the exercise pen. You can either add another barricade with space between so they can't get to each other, or attach something to the pen to make the openings smaller (as in attached photo).

Babies don't truly bond, so this is not at all unusual with the onset of hormones. They should both remain separated until both are spayed. Then they can be introduced all over again -- it will be like starting brand new. You'll just want to be sure that in the meantime, they don't have the chance to fight each other. Any hormonal disagreements or aggression they have now can sabotage their chance of bonding in the future.

Here's some more info on bonding. The photo below shows what I used to keep two rabbits from getting at each other through the exercise pen openings.

:yeahthat:
Your situation is indeed nothing unusual - your rabbits just aren't babies anymore. Bottom line is you shouldn't put intact rabbits together once they are weaned. At all. Ever. No matter the sex. They might look like cute cuddly toys but they can be nasty little monsters when their brain is controlled by hormones and a fight between rabbits can be really violent and bloody. The fact that there are both females doesn't make it any better - if anything it makes it worse, considering how territorial females can be.
You have to keep them completely separated for now. You 'll be able to spay in about 3 to 4 months, then you can introduce them again in a neutral territory after they've healed from the operation. I'm not crazy about same sex pairings as they are not very stable, but it might work if one of your bunnies is submissive.
Desinfect the bite marks well, just to be on the safe side!