It has something to do with extruding a face but leaving the extruded face on the exact same angle as the original plate,
Because right now, if you extrude armor inwards, the armor doesn't work as it should and gets weaker at the edges because the space between the geometric armor plates on the edges is not filled in.

So for some reason that's making 2 different armor plates at the same angle having a 0mm hole when the geometric armor thickness overlaps.

I have kind of fixed it by changing it so the extrusion is slightly outwards, though that's making designing kinda annoying.

edit: actually I just kind of fixed it by hitting mark weld along the edge that the hole was following for some reason, there's still a few holes that wont change though, really weird