She counted the pills and they are short 9 pills, 3 days worth

First of all, that just doesn't happen. Somebody took your pills. A friend, family member, repairman, landlord, etc. Your mom is right to be concerned, and to help you monitor your opiate intake. With any other type of medication, it might be inappropriate, but the risk of getting dependent/addicted to pain meds is just too high to fuck around with. It's a slippery slope where a person can start taking the pills a little more frequently, build up a tolerance, and not even realize that they've become dependent, if not addicted, and a person who is consistently medicated can easily lose track of their med schedule and accidentally dose too often, which increases the risk of addiction.

You need to enlist your Mom's help in figuring out what happened to your missing meds so it won't happen again. As it is, you're probably going to have to ration what's left and go without enough pain medication, at least for a few days until you're due for a new refill.

Your Mom is not your enemy in this situation; in fact, she's probably your best friend...