So I just ran into a combination bug/exploit.
First the bug: When at full resource utilization (i.e., no spare Durantium or whatever), I can't upgrade a ship that requires say 5 Durantium to another model that also requires 5 Durantium. Even though it would result in no net change in resource consumption, I think the game just looks at the upgrade requirements as if it were a "new" ship. A little frustrating, but I ended up getting around it when one of my ships was destroyed the next turn, freeing up 5 Durantium, allowing me to upgrade all of the remaining ships.
Now the exploit: So out of curiosity, that same turn (now that I had a pool of 5 spare Durantium) I tried upgrading 10 other ships that did not require Durantium to the model requiring 5. And guess what, it worked. The next turn I now had a -45 Durantium (and a massive money deficit*), but they all upgraded. Apparently, as long as you have enough for each individual upgrade, it doesn't matter how many upgrades you perform in one turn.
*Speaking of mass upgrading, it would be really, really nice if there was any indication at the Commands screen of how much a given masss upgrade would cost; there is such a number on the individual ship upgrade command, but not in the Governor interface...