If he's 3 months old, he might be old enough to breed. Lots of small breed rabbits (and some larger breeds too), are fertile at 3 months and sometimes even earlier. You need to separate them ASAP!
If you do want to breed them (which I really don't recommend unless they are purebreds of the same breed, you have researched a lot, and you can afford the vet bills from birth complications and caring for the babies), you can not keep them in the same cage! A female rabbit can breed immediately after giving birth. If this happens, you will have to wean the first litter earlier than recommended (4 weeks instead of 8) and the doe will be severely deprived of nutrients because she will be nursing while she is pregnant. It can also be dangerous to leave the male in with the kits. I might be wrong, but I think they sometimes kill the babies.
If you really want your first bun to have a friend, it will either have to be another girl or you'll have to spay her or neuter the boy. Otherwise those two should only be near each other when they're put together for mating and that's not much of a friend. And since it's difficult to bond intact rabbits, spay/neuter is really your best option.