It was from a bad mould process. About 60% of each hole had plastic from the moulding process left in them. I took a Carb Jet bit/tool at 0.065" and went through them to push/cut the excess plastic out.
If you look at the first photo, you can see the few circles that aren't problematic, but if you look at the other 98% the center looks significantly smaller.
Looking at the second photo, you can see all the holes are now closer in diameter.