I have been focusing on try to learn the Vasari the past few days so I'm sure if this is related to that race only or TEC as well. I did not notice this when I was playing the TEC for the last beta test phase however.

I paused the game and was reading some of the tech tree items and since I have many things enabled I clicked on them all and sure enough I was able to que them and went over -1000 for crystals. Then when I resumed the game it cleared everything back to 0 crystals but I dont think I got all the other resources back. Somebody else should test this I assumed it would que but I guess that is not the case.