I created an object which I copied and rejoined together (one-quarter of the object with a hole in it, copied and rotated it, and rejoined it together to make one object with four holes.
The holes that go all the way through are created using the Boolean modifier.
I tried to make another cut that only goes through halfway, which succeeded in the positive y-axis using a cylinder and boolean modifier. When I try the same steps on the negative y-axis it instead fills up the hole that goes all the way through.
I suspect that it has to something with normals, but I am not sure how to resolve this. I tried to recalculate the normals to the outside and I tried to clean up by merging by Distance (that last one solved an issue with the boolean modifier for the first holes on the negative x and y-axis).
Question: How can I resolve the issue that instead of substracting the cylinder Blender fills the previously created hole?