Sorry for the vague title, but it’s hard to explain in a short sentence. I made a simple gun with only two parts. A cylinder and a cube. I changed them around etc. etc. My computer’s OpenGL was borked for some time so I couldn’t texture them properly. I had to draw them in Blender. 
Once OpenGL started working again, I put on some textures. When looking from top view the cylinder is on top of the cube. If I pressed P then it would look like the cube is going through the cylinder at any angle. If I took off the textures and went back to drawing the textures in blender, it worked fine. Without the UV Face Select, I can’t really do much about it. Can anyone help? Thanks in advance. Also, here’s an image.
I know it’s textured bad, but that’s because I was rushing so I can make an image of the problem.