I'm willing to bet that the miles were deducted anyway (since unlike e500s that are deducted upon checkin, or CR1s or SWUs which are simply "reserved", miles are actually deducted upon an upgrade request).

I've already seen this glitch--except this was in person, at the aiport. Upon checkin the CSR asked me how I wanted to support my upgrade. I said it was already paid for with miles. It took her a bit of time to actually confirm that indeed, I had paid for this upgrade long ago.

My suggestion--check your mileage summary, and then email United to get this sorted out. With a bit of luck they'll refund the miles.