Does your son live with you? If not, does he have a key? If he has a key, he wasn't breaking in -- you just didn't hear him. In any case, this scenario should help you plan how to deal with a situation where you do hear someone breaking in, or where you realize that someone is already in the house.
If your son doesn't live with you but visits, then I would suggest a safe word or phrase so that you'll know it's him in the future. If you do wake up often in the middle of the night, make sure you're more aware before moving through the house.