Same here. -324 energy, -57 alloys. Fleet Stationed at a Starbase with Crew Quarters. Just cratered my game ( FanMil/Materalist Imperial, Starlit Citadel) because I couldn't figure out where the 'leak' was. Building another Alloy Forge or Electrical District wasn't making a dent.
Deleted my fleet of 20 corvettes, and the correct upkeep was removed (~16 energy, -3 alloys), leaving me "only" 308 energy and 54 alloys in debt, for ship upkeep on ships that did not exist.
Game Started on v4.0.3, played again on 4.0.5.