I think you're looking at this the wrong way.
Look at what Rodgers said re Moreno with City's 3rd goal. Rodgers was critical of Moreno for not pushing higher up the pitch and closing Navas down. Rodgers wants his fullbacks to be aggressive and if they're going to play like that you have to accept that from time to time teams will work their way around them and they'll get caught out. It's an occupational hazard. The fact that Manquillo (and Moreno down the left) are able to get forward but also able to recover is a huge positive. It's not by accident that the 2 fullbacks we've signed this summer both defend on the front foot, good in one on one's and have the pace and energy to recover.
As he gains a bit more experience and when we're playing better opposition, I'm sure he'll pick and choose when he needs to push forward or press high up the pitch and when he needs to sit in.
It's not that he's out of position too often - as you say, if you want your full backs to push on, this will happen. The issue is that I don't think that he is a particularly good defender when he is in the right place. People get past him, and he hasn't yet been shown up as he's fast.