If your soon underwent neurosurgery to remove a blood clot then he clearly sustained a serious injury at the time. He also fractured his skull. He may well have had a part of his skull removed in order to perform the operation, which would then have been replaced following the operation. The healing process will have left his skull a little bumpy, I suspect. I do not think this is anything he needs to worry about. If it is causing problems with the way his head is shaped with significant deformity then he can be referred back to his neurosurgeon too discuss further options. However, from what you say, it sounds as though these indentations are a minor result of what could have been a life-changing injury.