Holes are a negative in the first place: A not being within a certain being. It is a notion of difference.
Take a hole in the street, for example: Even if it is filled, it can be perceived as a hole in the street because the filling is not the same, no unity, with the street. But it does not have to be perceived as a hole anymore.
It is a matter of conceptualization: If I perceive the street as a plain unity, despite of filled holes, it is a street without holes. If I perceive the difference of the filling to its environment, I perceive it as a hole in the street, although it remains the very same street. But it does not exclude each other, otherwise we could not perceive a "street with holes". But without perceiving the differences as difference, there will be no holes.
And this is not the only problem within this: If my concept of a street is that of a flawless plain, because I never saw damaged streets, every difference will seem to be a "hole" for me (I take fractures out of consideration at this point). If I am used to see repaired streets all the time, only if it is not repaired (i.e. filled with proper stuff that a cars can roll over without a difference) it will be a hole for me. An asphalt street repaired with pebble and sand will be a street with a filled hole, whereas if it is repaired with bitumen it will be a repaired street without holes for me.
TL;DR: The more difference (from my concept), the harder it becomes to perceive a unity without this difference, therefore it becomes "natural" to see holes rather than "flawless" unity.
This, of course, pushes me away from any naturalistic epistomology or form of realism (Plato,Locke,Berkeley,Price, Russel, Searle). But that's okay for me, because I stick to transcendental idealism/constructivism (Kant, Sellars).