I feel like this has been around for a long while. What happens is when you click on a gravity unit to exit gravity, you lose alignment with your ship. You can easily get re-aligned my clicking the "space bar", but you probably shouldn't be losing your alignment to begin with.

I have some ships with simple vertical hallways with a gravity unit on the bottom, so I can turn off gravity and float up the tube, but I always have to re-align when doing this.