I just found (and replicated it 3 times) a bug where the weapon (Firebird SR in this case) just disappears from the storage after it was removed from a soldier and I tried to craft a new Magazine:
Relevant info:
Gun: Firebird SR
Soldier: Dhakiya Manson
Steps:
In the Personnel menu.
Remove weapon from inventory to the storage —This removes the ammunition from the gun.
Drag the removed ammunition to “Drag to manufacture” message.
Craft 1 or more ammunition from the displayed menu.
Once the you finish and return to the previous window, the weapon is no longer in the storage.