This is a bug that has existed in the game for a while now. The issue lies with re-shaping vs shaping. If you try to re-shape the weapon after getting all upgrades you'll encounter the bug. Instead you if you create an entire new Revision Zero it should allow you to apply all upgrades and craft it. I'm pretty sure that Bungie knows about the bug but it's extremely low priority for them because it's been months since the bug appeared.