subtractions broke mesh on specific angles

[doczoidberg]

I have strange behaviour that only on some specific angles of my meshes the result is broken. The red meshes are the meshes which cut the cube. Seems only the problem when 2 cutting meshes are near:

Sometimes all is right, an when chaing the rotation i sometimes get bugs:

What can I try? Also how can I check if my mesh is broken so that I could try an iterative solution?