I've observed a few times, while building things using Alienium, that the amount is deducted from the storage room and when you go back to Geoscape, you get a message saying the production was interrupted due to the lack of Alienium.
More specifically, what seems to happen is that if you have enough to build 1 of the craft/armor, but not enough to build 2, it will consume the resource without doing anything. If you have enough for 2+, it will just consume enough to produce the single unit requested.
Practical example:
Start with 15 Alienuim in the store.
Enqueue an aircraft consuming 10 Alienuim, the store drops to 5.
Return to Geoscape, and a message pops saying the production was stopped due to a lack of Alienuim.