How about this: if you absolutely have to have that last teeny bit of ore, try coughing up that excruciatingly expensive 250 common to build another storage tank!
Or as I said before, just realize that a few units of common metals don't matter in the slightest if you have 20,000-30,000.
Also, there isn't a single unit, structure, or even starship component in the entire game of outpost 2 that costs more than 10,000 let alone 20-30k. We haven't gotten around to creating unit stats and costs, but I still highly doubt this will change in OP3. If you need a ton of ore for something, and you want that little bit of ore, then if you've got the 25,000 to fill 2 and a half smelters (again, you should have 2 or 3 to begin with anyways, if you don't have that many at a point in the game where you need something that costs more than a couple thou, you're screwed anyhow so don't even bother building whatever it is, just hit alt+f4, you're cooked.) then just build the bloody thing, and then you've got your free space in the smelter to make use of that extra 150 common.
Seriously though, I don't really see this as being that big an issue.