I have actually had occasion to point out to an airline when upgrade certs were not properly removed from my account. And I was told not to worry about it. ^

I've also had occasions where too many certs were deducted, or a cert was deducted from me when gifting an upgrade and then from the gift recipient, and the process was too laborious to sort out and I wound out out a cert without benefit.

These things happen, and frankly they're too much trouble to chase down sometimes. They're best left to karma.

As dhammer53 says, you may well have been comp'd the upgrade. You might not have put one over on anyway. They may have decided they needed to upgrade someone so it might as well be you, no reason to take the cert when they were going to do an operational upgrade anyway. Or they might have decided that it was too difficult or time consuming to process the cert when they had other priorities.

Too many variables to lose sleep over these things. Sometimes we benefit, sometimes we lose, at least in my experience these things even out pretty well over time.