When you print with filament and you have a height that's shorter than the diameter of the extruded filament, that filament gets squished down to height you've specified. So my extruder is 0.4 mm and I have a layer height setting of 0.2 mm. So that extra filament gets mushed down. On the outside of the print it just makes the finely ridged surface but if you have a hole, that mushed filament will decrease the diameter of the hole a bit.As I see it, your best option is to run a drill down those holes if you need an accurate hole. If you are looking at a very accurate hole you'll want a reamer.