This is new behavior, as far as I know. Some anomalies will grant the player ships upon creation. Near as I can figure, the computer will auto design a ship on the fly for the player. All well and good. The problem is, it will use up a players' resources when it creates the "free" ship. And if the player has no resources? It'll display a "-1" in the upper right hand corner of the screen.
Logically, these free ships shouldn't use up any resources that the player has at all, I would think.
So far, I've seen this for Survey ships granted by an anomaly (specifically the "prototype survey module"). Here is a screenshot of a newly created survey ship at the beginning of the game causing my faction to have a "-1" in Thulium.
I have a save file created just before getting this survey ship. If this is indeed a bug (even if "free" ships are supposed to take away my resources, they shouldn't put me in debt), I'll send it to Stardock when I have the chance.
