As the saying goes, "no good deed goes unpunished".

UA tried to do the right thing here. The other option - and the correct one as per their UM policy - would have been to have denied boarding (or more specifically, denied check-in) at the origin airport.

Instead someone decided to bend (break?) the rules, and it came back to bite them - mainly it would appear due to the mistakes of the EW agents who incorrectly allowed a non-manifested passenger onto an international flight. (Yes, it seems there were other mistakes - but that's the one that was the most egregious).

From all accounts, the UA agent took the passenger to the gate listed on the boarding pass, handed him off to the gate agent there who then gave him someone elses boarding pass and then allowed him to board without properly checking the passengers passport.