When you take a resource from a storage silo, a little slider pops up for you to put how much you want. If you want more than you have enough room for, it just puts in what you can carry.

Vaults don't do this. Instead, they just throw up the not enough room message and won't let you take any of the resource. You have to split at least one of them away from the rest of the stack, put that in your inventory, and THEN it will put in however much you can carry. It's not that many more steps, but the inconsistency is still annoying.