For what it's worth, at about upgrade level 50, I also experienced negative numbers with Stronger Explosives, and once with Faster Antiair Reload on my Droid. I was at about game level 900 at the time.
It does not occur all the time.
When it occurs, I get my upgrade, but my upgrade points actually increase by about 40 million, and the upgrade cost is now -40 million or so. When I upgrade again, I get my upgrade and my upgrade points increase another 40 million or so. I do this 6 to 10 times and finally I lose my upgrade points.
Another error that I'm seeing is that when I play a VR game, I may earn 50-60 million points, but I only get 20-30 million added to my total. Points work fine in the basic game.
I do not know if version 1.3 fixes these errors.
I still love the game.