As stated, all NPC fleet ships are un-salvageable when they are overheated.
The game seems to think they are made entirely of Cores, as it throws the "must salvage core manually" pop-up when attempting to salvage any block of it.
A work-around exists:
Add the overheated ship to a fleet you own, you can then salvage it.
As such, the actual problem seems to be the game not removing the fleet ident when the ship overheats.