I came across this bug in a much different way, I imagine it could be related. However I could not replicate this again.
I created a drone miner, and set it to mine near an asteroid until I could upgrade it. I upgraded it after removing every block except the core. I rebuilt it using more blocks. I left the sector and asked the fleet into formation. As my drone reached the flagship the outer edge was the new ship, and the center was the old ship. Both were merged together.