The problem has appeared again.
One screenshot shows 19 ships (Corvettes) ready for retrofitting.
The second and third are the fleet manager.
The upgrade is zero point reactors which need to be manual applied to federation ship presets, despite having auto-upgrade checked. Not only that once retrofitted the rest of the fleet will be able to follow suit once the initial upgrades have be carried out. I overlooked this previously as I was unaware of its importance.
I'll provide a screenshot for that once the fleet returns home
Edit: Only the Corvettes have been retrofitted. Destroyers and Cruisers have no option to do the same. Last three screenshots are mid-upgrade followed by it's results, and post-upgrade.
Edit2: Updating ship presets cause an entirely different ship to be created despite sharing the same name. Screenshot provided uses a Destroy class ship (one with auto-upgrade applied and the other disabled)