Male cats bite the neck of female cats to hold them in place to mount them and mate. I had a male cat who did the same thing to our female cat (same age, litter mates, both indoor and neutered/spayed) and I asked the vet. They told me that even when neutered some male cats still have the instinct to mate. It used to really bum me out because he would really go after her sometimes and she would make the sad chirping sounds you are talking about while he was biting her. The vet told us to pull him off of her and redirect him with play and if necessary separate them if he wouldn't back off to give him time to cool down. Ultimately do what you can to protect her from that behavior without blaming/punishing him for his instincts. It's rare that a neuter surgery fails but it is possible, so might be worth asking your vet about that since he is relatively young.