Ok, I got a repeatable version of the problem, captured in
this zipped save game.In the upper right of the map, there is an orange fleet called "Trouble", containing two vessels, 'Outlander', and 'Gwinavere'.
Choose 'Outlander', go to it's details and upgrade to a 'DD Guideon-1103'. Then de-fleet the upgrading ship. It will disappear from the game.
Something that may be worth noting is that as soon as it's upgrading (but before de-fleeting it), the hit points are negative. Also, the single remaining ship won't move for a week, as though it's somehow tied to the upgrading-for-a-week process.
Also, an entry appears in the ship list for the upgraded Guideon class destroyer 'Outlander', but there doesn't seem to be a ship on the map that it corresponds to. Centers on the square the fleet was on, but no ship.
Hope that helps.