Wild rabbits can go anywhere on the continent and start a new warren if they don't get along with each other, but they are social animals. Fights, chases, fur plucking, humping is quite normal behaviour for rabbits, but running away too. Girls mostly do it to establish a pecking order, make clear who is boss, males more to drive a rival away, their fights escalate more quickly. They live in groups because survival is easier than alone.
If there are 2of them chances are 50% that the fox eats the other guy.
Also, the does determine if and when they want to breed or not, and they breed several times a year, lots of offspring of which most dies young. Live expectancy of wild rabbits is about 3 years.
Our rabbits can't just go away. Your doe is like a teenage girl, enthusiastic that she has her own room, just finished decorating the walls with boy band posters - and then someone puts a small boy into her room - understandable that she isn't thrilled about that. She's hitting puberty, and that urge to establish a hierachy and defending her little empire comes up, and depending on her character or how long she lived with her littermates to socialise and learn how to deal with other rabbits that can be more or less violent.
Somewhere else, not in your little girls teritory, it might go smoother.
Your second bunny is very young, that may add to the problem, normaly, kits aren't attacked by other rabbits they are familiar with, be it other adults or kits of the same group, it's the change of circumstances we humans confront them with that can cause problems if not done right. The poor boy has no idea what's happening, doesn't understand why that rabbit is mean to him.
Your buck might become fertile in about 6-8 weeks, if they are together then there'll be baby rabbits, 4 weeks later the next litter, after a few years the world would be covered with rabbits 3 feet high. Since this didn't happen yet, a lot of dying, killing, suffering, starving, diseases, predators, parasites and so on is necessery to keep them in check.
Breeding rabbits can get out of control quickly if you don't know what you're doing, and that can become quite ugly. Keeping them together without neutering at least one is not an option. Can't tell which one to neuter if not both, all my rabbits are intact, so I can tell you that leaving a door not properly latched for 30 seconds ends in more rabbits than I can eat. My house bunny (no cage) is a buck now, no problem, had an intact doe in the house for half a year, gnawed everthing, peed everywhere, and was quite destructive (well, this one defintly is a special girl...), neutering normally reduces problems like that.
You're right that a single rabbit might feel lonely, here it's even illegal to keep a single pet rabbit (stupid laws here), it really depends on the rabbits character, but most are happy enough alone.
Maybe someone can point out a vet if you add your general location to your profile.
