When you hover over the crafting window on (at least mk1 factories i haven't been able to test the others) factories aren't highlighted to show that you already have them in your inventory. Minor bug but I figured I'd report it anyway

This is because those factories you have in your inventory are technically different item types, because you already built them and picked them up. Note that those in your inventory say Factory Mk1 (inactive) instead of just Factory Mk1.

I figured that was the case, though I tend to rely on that mechanic when i'm looking for something in a busy inventory.