UA can't involuntarily upgrade you and then charge you for the privilege. (In general you don't have to pay for services that you don't order and didn't impliedly order.)

The "Add/Collect Difference" may be a preprogrammed statement, that the computer spits out as a reminder to someone (clearly not the FAs) that you have been seated one cabin higher than expected -- maybe the computer picks up any mismatch between Y fare and 3-class F cabin, and then prints this tag on the manifest for the use of the ticketing or gate agent.