Sounds like they need a timeout by: The Greek Tortoise Guild
This generally isn't a problem with a male and female tortoise that have lived together for a long time or are at least accustomed to living with other tortoises. Did you put them in the same enclosure relatively recently? Is your male a lot bigger than your female? These are commonly problem situations that can lead to injuries or at least aggression. Either way, it sounds like they need to be separated or at least placed in a much larger home. Depending on your situation, one may be more feasible than the other. You will have to decide which makes sense to try first. But, if you try putting them in a larger enclosure and she still is getting injuries from him then they simply can't live together. The only time, then, that they should be brought together is when you want them to mate, and then they should still be watched closely. This is all assuming, of course, that they are of the same species (NEVER PUT DIFFERENT SPECIES OF TORTOISES TOGETHER--THEY CAN SPREAD DISEASES AND COULD INJURE OR KILL EACH OTHER). Let me know if this is helpful or if I can help with anything else by replying to this post or by going directly to my blog at TheGreekTortoiseGuild.blogspot.com Good luck!