I'm not sure if it was "no problem", necessarily. United/Mourinho were successful in preventing City's attacking juggernaut from scoring from open play, and even really taking very many good shots (relatively speaking). If Lukaku hadn't made two defensive errors during those set pieces and all else being equal this match ends 1-0 to United and the narrative is very different.
Could Agüero have made a difference? Hard to say. Clearly Pep didn't think so. Or, he felt Sterling was better for the pseudo-false 9 thing he was sort of doing.