Making a thin section isn’t exactly a gentle process. The small-scale violence of grinding is what gives biotite and muscovite their characteristic birdseye extinction. Some minerals are prone to developing holes or just plucking out all together (I’m looking at you, apatite). Even quartz, that most stable mineral at Earth surface conditions, can fall victim.
Holes can be distinguished from other featureless (PPL) or black (XPL) things by their low or negative relief, and they’re often surrounded by minerals’ raggedy edges. Except for apatite, which has the weirdest ability to pluck out without affecting its neighbors in any way.