Since I'm not a UAL employee this can only be my opinion, but there is NO risk that the Milan agent would be in any trouble. This type of operational upgrade is routine, though not "common".

You certainly can complain. The pickle you're in is that it's the gate agents that ultimately control your fate. If you do complain and you encounter that gate agent again, you might find yourself back in coach the next time. My philosophy is I NEVER argue with a gate agent. I have disagreed with them politely on numerous occasions and have had some success at either achieving a double upgrade or an upgrade for my family members who were traveling with me on award coach tickets.

If it were me, I'd probably try to work the situation through Mileage Plus, not United Customer Relations. You might be able to find someone at MP who would spring for some upgrades for you....

Good luck.

p.s. You're also correct, the gate readers will take any boarding pass as long as it's for the flight currently being boarded.