In mission 14-Galactic Rim (Gulf Sector) after the MCV docks with the Ragnarok and returns it would take up an additional 6 support units, 3 if using a single Mimic. It happens again in level 16-Sojent-Ra System (Far Reaches Sector) when a Worker docks with the Clee-San using up another 4 SU.

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.

Does Emergence fix this bug?

I have never seen this bug in any of my playthroughs of the game, so it was most likely fixed way back in the 1.01 patch.

I was playing the 1.01 patch when I discovered the bug. That was 5 years ago, I think. I only noticed it myself because I was making a walk through at the time. Watch your SU count carefully in those missions. Or try to retire the full fleet and see if you can reach zero.

I made a work around that involved editing sMCV.shp, sMimic.shp, and sworker.shp for use during the specific cut scenes.

I also encountered ship modules becoming Independent. In mission 12 after the Outpost surrenders the modules on the Command Ship and Carries had their own health bars. If I selected the Command Ship, either Carrier, or the Outpost all 4 of them and their modules appeared in the selection list. It looked like the modules could be upgraded but only 3 of them on the Command Ship would have a progress bar.