You're right. In fact, it depends on which navigator you use (which is why some people can finish a map in 4 "seconds", while I am unable to do it under 15 "seconds"). I don't understand why, thought...
In the shop, if I set the sell amounts to as high as possible, then decide to upgrade my equipment instead, I can go back to the shop and sell as many of my resources as I had before I used them to upgrade. Which, naturally, leaves me with negative resources.
Thanks for letting me know! It's fixed now.