Only seen this once so far (happened today).

Situation occurred while I was in the tech tree.  I purchased several techs (had quite a bit of money at the time), and went back to the main screen to build something.  The game wouldn't let me, telling me I lacked sufficient funds.  I looked at my cash and found it reading something like -3159.  I thought at first I went hog-wild buying tech, but I had something like 25k in cash and only bought about six mid-level techs, so I should have had plenty left over..and besides, I'd never seen the game let me spend more money than I had before.

So, I saved the game, quit the game, then reloaded it, and that fixed the problem--cash was back to a positive value that I think was correct.

Not sure if it's helpful, but I was playing the small random galaxy as TEC vs a normal CPU playing Vasari, and pirates were active (all setting were defaulted).