It can be because of 2 reasons,
- Sharp tips present on the 3rd molar of that side.
-the upper molar is out of the arch, so while bitting it bites the cheeks too.
The cusp tips needs to be smoothened, so that it won't poke while biting.
Health Tips
You can apply topical pain relieving gel for it subside quicker. But the correction has to be done too.