Heh.
I am very familiar with this and no, there's no wastage.
That number is just your change in the amount of resources you have stored assuming non-zero resources.
If you hit zero resources, all building projects slow down enough so that your effective resource consumption is +0. Whatever you are building ultimately takes the same amount of resources, it just takes longer to build because your engineers can't work at 100%.
That does raise a question though. Say you are getting into mid game and have a decent sized economy which you then strain by bringing a golem online so you only have +10 metal after your power generators take their cut. You then get raided somewhere losing a bunch of metal harvesters, but no power generators, so you don't have enough metal for your power generators, what happens?
Note that this isn't you not having enough power generators, this is not having enough metal to feed the power generators you have built. Does this shutdown power generators until you get the metal harvesters back? No effect? Everything shut down?
Actually, this sounds like an experiment worth trying.
D.