Indeed. Something very wrong there... At the very least, Boeing should have an inspection team at Spirit Aero double checking them before they're loaded for shipping and once again once they get to final assembly.
Better yet, bring the fuse assembly back in house.
Obviously, starting with the wrong aircraft hasn't helped 
It's a pretty basic quality failing, you would expect them to weigh the assembly as part of the QC to make sure there is the correct part count as a minimum.
Weighing the door wouldn't have helped as the bolts would have been removed to get the door assembly off for weighing...
Boeing and Spirit bang to rights as the door was removed during final assembly in order to allow Spirit techs to rework 5 rivets. Photo evidence taken during the post rework reassembly shows the interior being reassembled with the door back in place and ALL four bolts NOT present. It's a wonder that the door hadn't already popped open during a rough landing.
Whether the oversight was criminal or not is upto to the NTSB to decide, but someone screwed up and someone else failed to spot it. Even simple maintenance tasks are checked and double checked to avoid this very thing.
Unfortunately, with the potential increase on A320 family production as a result, the chances of this same thing happening at Airbus are statistically quite high.