Hard to say what the problem is. is there a cave for the puffer to hide in? if not you need to provide one so the fish can recluse to a quiet area where it feels safe. do you feed your puffer shell fish on the shell? is the temperature and water parameters all good. The fish could be wanting to get out of the tank or move away from something that is bothering it, it could have a gill flukes problem, the damaged area may be stressing the fish. really hard to say. you will need to treat the fish for gram + and - baterial infection as a precaution. look very close and see if you can see anything at all, redness around the wound, any thin strings, lumps, bumps, bleeding, rapid respiration, swiming problems, eating problem, any other things not mentioned. also try to cover the corner where the fish is running up and down sort of like a cave open to the tank and see if that helps. look in the room and block the fishes view of various items and see if it stops at any time. good luck and keep us posted. others may weigh in here too.