I made a new mission, moved my ship off to the side, spawned a cain and some cargo's at specific range increments to see how far the ship "drifts" after it warps in as part of the mission I was just starting. I loaded up to a strange sight. I had no weapons and no display at the lower right of my shields and hull. Further more I was dreadfully unmaneuverable and completely stationary. I used the outside camera to see that I was one of the cargo containers.
I deleted that container. I moved to the next one in line. I deleted all of them. I was the cain. I deleted the cain. And here's where it gets interesting. My weapons showed up as normal but I was completely stationary in all regards and the camera kept shaking violently, until my ship warped in (I now noticed what was supposed to be my ship warped in after several seconds instead of being there from the start). Stranger still, was that my engine energy kept increasing and I was gently drifting about and I realized that the AI (that had taken control of my ship when I was the containers and cain) was still in control, but I was as well. I could move around normally, yet always the AIs neutral "milling about" movement continued, and he would always continue increasing engine energy despite attempts to fix it. Starting a new mission did not fix anything.
I apologize if this is a well-documented bug, but I would like it some sort of solution this dilemma.