When I attempted to dock this ship using the command "Carrier Recall," It would not dock and would continuously bug out for about 3 minutes, at which point it decided to dock. I had docked the ship manually before hand with no problems. I am not sure, but this bug may be related to the location of the rail docker.
Enclosed is a clip of it. (.AVI)
Attempt to dock a ship using the "Carrier Recall" command in the Fleet System.
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Thank you for the video, you can easily fix this issue.
Use your pick up rail so it's not that close to your main ship, put that pick up point at the beginning of the pick up rail so it tries to dock 10 blocks or so away from the main ship.
What you're seeing is the ship trying to avoid collision with the main ship, it can't dock since the pick up point is too close to it.
Going to reject this task after it works again for you, this is something that will get worked on soon.