Females are notoriously territorial. However it is rather unusual for such young rabbits (6 weeks?) to not accept another rabbit. Typically (but not always) all baby rabbits get along.
There are a couple problems/difficulties with what you are trying to accomplish. First and foremost is that all the rabbits are young. This is not the time for bonding. As mentioned, most baby rabbits get along, but this is not being bonded. As soon as hormones kick in, all of that changes. If you only had the two sister Flemish rabbits, there is a real possibility that even they would have a falling out with the onset of hormones. So, in short, baby "bonds" don't count as true bonds and are not any indication of whether or not they will bond in the future.
What is the age and neuter status of the Lionhead?
The second difficulty with a trio is that rabbits arguably do best in bonded pairs. But if one really wants to have a trio, that is best attempted when 3 rabbits are already all fixed (and healed) and all meet each other for the first time as stranger rabbits. That meeting should be in new (neutral) territory.
You are correct in keeping the Lionhead separate from the other two now since they are not getting along. It's possible (likely?) that she will continue to have to be kept separate. Perhaps, in time, she could be bonded with a different rabbit. If this happens (or even if she is kept single), the 2 Flemish should be housed in a totally separate area of the home. The presence of a 3rd rabbit (or pair) can negatively affect the bond of the 2 Flemish (and vice-versa). Rabbits don't like having non-bondmates anywhere near their territory.
