Yea this happens to me. I find it confusing.
I had a dock where i had more enhancers on the x-axis and less on the y-axis so that my ship would dock with its length following the x-axis. Weirdly, it did the opposite. Which means that the longer part of the docked ship is on the docking side where the enhancers were not enough to suppport it. Kinda confusing on writing this but I hope people can understand.