Because I'm a behaviorist not a veterinarian I can only address the behavioral possibilities.
Yes, it is absolutely possible your cats could have gotten in an altercation in your absence and Mittens suffered wounds. When my husband and I first moved in together years ago with his 2 cats, my 2 cats and 3 dogs, one of his male cats bit my female cat on the tail. We didn't witness the event but we pretty much knew which cat it was most likely to be.
However the hair loss could also suggests she is licking/grooming herself excessively for whatever reason - in reaction to social stress among the cats, allergies, or some other skin condition your veterinarian would need to diagnose. Without knowing exactly where the wound/hair loss is, it's hard to know whether it could be self-inflicted or not - e.g can she reach the area herself?
If the hissing and swatting during the introduction period were fairly frequent, and are ongoing, there's a good possibility that the cats really don't like each other that much yet, and while they may choose for the most part to avoid one another, if one feels (or actually is) trapped by one or more of the other cats, the behavior could escalate to biting.
You didn't say whether you did any systematic introduction of your 2 cats to your boyfriend's, but we recommend very gradual, controlled introductions - we give a step by step plan in our Helping Kitties Co-Exist DVD available at HelpingKitty.com
If you don't like your veterinarian's assessment of your cat's wounds you can always seek a second opinion from either another general practice veterinarian and/or one who specializes in dermatology. The hair loss I would think needs to be evaluated. Your veterinarian has seen many more bite wounds than you have so his call may be right on, but it's always your right to seek a second opinion if your are unsatisfied.
I'd also use the resource I mentioned above or others that you may find you like, to start working on the relationship among your cats to help them be more relaxed around one another.
Oh! Forgot to mention, Mittens is also losing hair in about a 2 inch radius around the wound, on both sides.
I would concur with Dr. Hett's assessment that if you are concerned about your veterinarian's diagnosis, you should seek a second opinion. Unfortunately, since we are conversing over the Internet, our doctors won't be able to see your cat and help make a diagnosis, but they can certainly offer some advice and personal experiences of what they have seen in the past.
I would encourage you to return to your regular DVM or find another for a second opinion soon. Cat bites are notorious for forming abscesses. Did your first veterinarian prescribe any antibiotics?
One final note, and remember, I can't see the wounds, so I am just throwing out another idea for you...did your veterinarian find any fleas on any of your cats? Symmetrical hair loss at the base of the tail is often associated with a flea infestation. Even though they don't go outside, fleas find ways to get into our homes...your boyfriend's home could even have flea coccoons from a previous infestation.
Good luck with your cats! Having multiple cats is very fun ( I have had up to 12 at some times in my life) but it also comes with some frustration when everyone fails to get along!
I'll give a bit more info, but thanks already for the responses!
The three cats had a very systematic introduction when they first met 6 months ago. They did frequently hiss and tussle when they first met from between doors and such, and occasionally once they were together. But that hasn't happened at all frequently for at least three months.
Her hair loss is occuring on her rear, close to the base of her tail. It stretches from her anus on both sides up at least three inches, about an inch or two wide in some places. She can barely reach that area readily, though she is very protective of it. If either me or my boyfriend try to touch it to investigate, she gets very upset and tries to get away, sometimes growling.
The vet did check for fleas, I believe, with a small-tooth comb and examining the fur. He found nothing, and I haven't seen any scratching of any of the cats. Should I get maybe a flea collar or flea medication just in case? And yes, he did give me antibiotics, as well as tapazole for poor Mittens before her surgery. I think after she gets that done, if she's still having the issues with hair loss, I'll have the vet double check, since the surgery is coming up.
Thank you both, for your advice and the good luck. I've always had at least two cats since I was a kid, and can't imagine a house without at least one!
Next time you go to the veterinarian, take Octavia along with you. Have the staff "flea comb" her as well.
Again, since we can't see the cat, there is no way to know for certain, but if Mittens has any sort of flea allergy, you generally won't find fleas on her. Pets who are allerigic to fleas are VERY good at catching the little pests...that's why we see hair pulling and hair barbering in these animals. They will groom and bite and scratch until they find the offending flea. Other animals in the household, those without flea allergies, may not even notice that they have fleas. One of my Siamese would pull all the hair out along her inner thighs, backs of her thighs and along the base of the tail. We finally had to take my Himalayan in to the veterinarian in order to diagnose the flea problem.
Keep us posted as to how things progress!
It's clear from your cat's reaction when you try to touch that area that it is painful to her. And that's a significant amount of hair loss you describe. So, it's good that you are taking steps to find out what is wrong, because she is experiencing discomfort that you need to get to the bottom of.
I wouldn't use any flea medication or topical stuff without your veterinarian's input especially since Mittens has recently had other meds for her surgery. Mixing medications without your veterinarian's input can have really dire consequences.
Again, I'm not a veterinarian but from you initial profile you say your cat suffers from hyperthyroidism so that's another thing you veterinarian should be rechecking as well.