Often, changing the order in how the operations are done can fix these issues…
For instance… joining all the smaller cut out objects into one object, then subtracting that single object from the large mesh.
so instead of A minus b, A minus c, A minus d…
you could try A minus ( b plus c plus d )
Changing the order of these operations can also make the CSG faster… you’re trying to balance where/when the heavy operations happen. it’s somewhat of an art.