You should separate them from each other. Two separate living enclosures with at least a space in between, as rabbits have been known to mate and harm each other through a cage wall. Since hormones have emerged, they may fight each other and/or mate, if one of them is actually a male. Both males and females hump, so unless you see one of them has descended testicles, then it’s a bit unknown without an experienced rabbit vet.
What they had prior to this point is what’s called a baby bond. When rabbits are young and without the hormonal urges, they tend to get along very well with each other. Once hormones hit, problems may emerge suddenly and former cuddle mates may have a bad relationship.
Presuming neither are pregnant, they would need to both be fixed and after recovery, you can begin the bonding process. You can find more information about bonding in the RABBIT INFO section of this website. The fact that this has been happening for 1 to 2 months makes me feel like they are both the same sex. I feel a pregnancy would have happened by this time.
Unfortunately, BB forums prohibits the discussion of intentional breeding. As a result, majority of our members (me included) are pretty naive to the timeline and methods of identifying pregnancy. I know other forum leaders may have recommendations so I will allow them to elaborate their knowledge to help you!
… misgendering rabbits is very common, so you are not alone in experiencing this!
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.