It seems like the problem was actually the camera and not the position of ships. It seems that depending on what action I was doing with my craft before the camera manipulation kicked in caused the orientation of the camera to change. Using reset-camera immediately before doing any camera manipulation seems to have solved the problem.
Edit: nevermind, the camera is still occasionally not obeying me when I have to focus on specific positions. I can't even begin to imagine what is going on, it just does not seem to like set-camera-facing and decides to have it face at the wrong position randomly with no consistent pattern. Maybe I'll try using set-camera-target instead.