This is probably related to the fact that I've noticed that when you dock while moving, the game doesn't appear to update your position according to the movement of the base but rather according to what you were doing before. If you have your radar up, you'll notice it doesn't stay centered on where you are. Below is a fantastic example. Notice the distance to the object i have selected on my radar screen.
Attachment:
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Another issue that is probably related is that sometimes when you remotely toss something from one of your docked ships, the debris sometimes appears not on top of the AI base but some arbitrary distance away. (seen over 1k before)
The reason this is so apparent when dealing with emp bio is that your client and server don't talk as much when you don't have an engine equipped
(or so my theory goes...) so the disparity grows much more apparent.