I am currently working on a 3d game in Unity, and I am working on the level design using ProBuilder. I basically created a huge cube which I "flipped normal", and a second one way smaller which, as the other one, I flipped normal, but as soon as I crossed it while turning backward I could weirdly see through the small cube, which makes it feel unfinished. How could I fix this issue?
Normally in 3d games triangles can only be seen from one side. Usually this is not a problem because walls have some thickness. Since you clearly have paper thin walls made of only one layer of triangles this is exactly the result you should expect.
In short add the other side to your walls. The simples way is to duplicate the existing triangles and flipping them. Walls will still be paper thin of course. Later you should probably make them thicker.