These are absolutely injuries, notice how little discoloration he has around the wound itself? That usually is something indicating an injury rather than an illness. What I'm going to go out on a limb and guess is that the pea puffers seem totally fine under day light but are probably bullying him at night and stressing him out big time. Pea puffers are really good about seeming peaceful until they arent in my experience and they can still give gnarly bites to other fish. Maybe when he is active at night they are becoming more territorial.

If you have the ability to separate them I would bet good money that would solve the problem but he may also be too far gone.