I read some saying here that passport check at counter just before boarding is a Canada specific requirement. It is not Canada specific, at-least for the countries I have traveled to. For all my UA (or non UA) flights to Canada, India, Brazil and Germany from the US, all passengers were asked to step up to the counter at boarding area where their documents were re-examined and their boarding pass initialed by the GA. This is regardless of whether their documents were examined at the check-in counter.
So a question to OP is if he/she had his passport rechecked at the boarding area or not? If no then UA did nothing wrong here, but if he had (and his BP was initialed) then this is something to be discussed about.