When you use the hammer to break a Compact Ore, it breaks only 1 of them. If you use it on the rock or ore next to it, it will skip breaking the compact ore though the harvest level is OK.

Compact Ores

It's not that bad if the compact ores are not that many, but I sort of wanted to increase them even more, but if you can't hammer them it's kindof a problem

Unfortunally it's a compact ores bug. They already fixed it a few months ago but didn't release it. Here you can see their fix: DoubleNegation/CompactOres@f1903ac
I tested with this version and breaking worked properly.

Now I saw that you already reported it to them at DoubleNegation/CompactOres#26 :) nice!