My game is patched to 1.01.
In mission 14 after my MCV docks with the Ragnarok an additional 6 support units are taken up, 3 if using a single Mimic. I retired or scuttles my entire fleet but I can't recover those support units. It happens again in level 16 when a Worker docks with the Clee-San. Another 4 SU are used up by nothing.
I think when the cut scene starts the ship is converted to an allied unit instead of a player controlled unit. Afterward it's converted back and it adds to the support count again. Except the SU were never deducted in the first conversion. So there's no longer a ship that they correspond to.
I tried scuttling the ship just before the cut scene starts to deduct the SU that way. The cut scene froze at that spot with no ship to follow. I had to force the game to close.