This is actually normal, and I have had it happen to me. You can have negative resources depending on whether or not you traded for them and how you used them.
For example, if you started with 0 Durantium, traded with an AI for 20, used all 20 in ship building or Durantium Refineries, and then declared war on the AI that you got the durantium from, then your quantity will go to -20. This is because when your treaties involving these resources end, unused resources return to their original owner, and declaring war is the quickest way to end treaties. Essentially, you "owe" resources.
