The Liberals did indeed win the popular vote; they got more votes than any other party in the last election. If the popular vote in the US presidential election had been Trump 45, Clinton 44, others 11, there would be no question about Trump's legitimacy. It's not the fact that he didn't get a majority that's in issue, it's the fact that he didn't even get a plurality.

In Canada, the fact that the governing party didn't get an absolute majority of the popular vote IS used to attack its legitimacy; this was true when Harper was in power, and it is true now. Imagine the response if one party managed to get a majority of seats while getting LESS votes  than the Opposition party.