I’ve noticed that too, my vacuum would always leave small dirt patches even though everything looked fine mechanically. What fixed it for me was checking the vacuum head brushes; a few were worn down, so it wasn’t making full contact with the floor. After replacing them, it started picking up the finer stuff much better.
Also, if your water flow is too strong, it can actually blow lighter debris away instead of sucking it in. I turned my return jets slightly downward and that alone made a big difference. Sometimes it’s just small adjustments like that, good suction, clean filter, and solid contact with the floor, that get rid of those annoying leftover piles.