Sometimes it's not territory so much as the individual personalities and the experiences of the two rabbits involved that leads to a fight. Some rabbits who have never had a friend before, for instance, have very little experience socializing with members of their own species, and are either unable, or afraid to, react to the new rabbit in an appropriate manner. This was the strategy employed by Macabee when he arrived in my foster home. The problem was compounded by Macabee's belief that he should be the dominant bunny in an already established group, a feeling that was not shared by all the other rabbits. The result was a series of wounds suffered by both Mac and some of the other boys, but the greatest wound was probably the one to Macabee's ego.
On the other hand, as I mentioned, rabbits can pick fights with their friends too, and it's often difficult for the human to tell what set if off. Sometimes it's as simple as smell. If one rabbit had to go to the veterinarian, especially if he had to stay overnight, sometimes his partner will not recognize his smell when he returns, and will attack him. Sometimes rabbits will fight if there is a change in one rabbit's status, or if the rabbits are of different ages, and one reaches a different stage in his development (most commonly this occurs when a rabbit reaches adolescence or maturity), the relationship may have to shift to reflect the change, or else a fight might break out. Sometimes a rabbit who had been submissive for his entire life might decide that this is no longer the case, and will challenge his partner's dominance, leading to a fight.
Fights can also occur for what seem to be petty reasons, such as when rabbits fight over snacks. Usually these are minor tiffs, but if one rabbit is mad enough, it could turn into a full-blown war. Especially when the relationship was relatively sensitive to begin with, marked by a lot of bickering, small insults and subtle offenses can sometimes flare up into major battles.
How do you know when a fight is brewing? Some unmistakable signs of impending hostility are: tail up, ears back, growling, sometimes thumping, an angry look in the eyes (you know it when you see it), jutting the nose and chin forward, agitated sniffing, and a generally tense posture. If one rabbit doesn't back down, or a person doesn't intervene, this is usually followed by the preliminary moves: circling (sometimes followed by humping), chasing, boxing, and jaw-snapping. After this, a full-fledged fight breaks out, marked by biting, kicking, jumping, and boxing.
How do fights resolve themselves? Rabbits in the wild fight to establish dominance, to keep newcomers out of their territory, and (for females) to protect their young, so fighting serves an important social function. So while fighting is "natural" insofar as it occurs among wild rabbits that doesn't mean that we should allow our domestic rabbits to settle disputes this way amongst themselves. It can be very dangerous to allow rabbits to fight it out at home, because the wounds can lead to nasty, abscessed infections. In the wild, a rabbit who is not accepted into the warren will leave, whereas our pet rabbits don't have that option, thus territorial fighting, for example, will only lead to injury
http://www.rabbit.org/chapters/oakland/fight.html
Hope this helps you understand why it might be happening. You may need to seperate them and then slowly re-introduce again as if they were meeting for the first time!