There is also the possibility that something stressed the mother, so she harmed the baby. By the location, it sounds like an accident in moving him about, but just in case, where is the hampster located, how quiet is it, is it nice and dark there, and are there other animals around? If it is too high traffic, too loud, too bright, and if she can even smell a predator, the stress could make her harm the offspring. Honestly, excessive moving of the babies usually means the mother feels insecure about where they are. I've never seen a rodent with a large, well-placed, secluded cage move the babies until they simply got too big for the old nest site. So, something like (carefully) relocating the cage to someplace warm, dark, and quiet, or even just placing a towel over it and only disturbing them for food and water, might help.
If the baby is old enough to be handled, you could at least keep the wound clean with a mild saline flush to see that it doesn't get infected. Don't put any ointment on it however, as sometimes other rodents find these "tasty." I've heard horror stories about mice cannibalizing cagemates being treated with ointments, and my own mouse anja got attacked when I started her on her eye meds. I'd imagine hamsters could have a similar reaction.
Good luck with the lil guy. Hope he pulls through
