Yes, I have experienced the same where my VIP upgrades were incorrrectly reduced. A quick call to the EXP desk and they took care of crediting my account. It took a couple weeks, but was done with no hassle.

I guess if you are desperate for an upgrade and have no VIP's left, wouldn't hurt to give AA a call and see if they give you an upgrade on someone else's dime. Not sure how that would work out in the end.....