I DO want them to have babies so that’s not the problem
Why would I separate them?
Here are my answers for why you should separate them now:
she probably is pregnant, although it would have been better for her to grow up a bit more first.
Having the male separate ensures that he will not breed the doe (if she is not pregnant yet), does not trample babies when they are born, and does not rebreed the doe after she gives birth. Yes, a male rabbit can rebreed the doe before you even know the babies have been born, if he is in the same pen with her.
If she isn't pregnant yet, it would be much better for her to stay not-pregnant until she is at least 5 months old. (Larger breeds should be older yet, but Lionheads are usually small, so plan on 5 months minimum before you let them breed.)
It is also best if she has a break after one litter before getting pregnant with another litter-- and that will probably not happen if the buck is in the same pen with her at that time.