There have been credible leaks that this was a management level problem.

They specifically didn't want the aircraft to be inspected - as it had already been inspected and doing it again would have delayed delivery... so they had a policy in place where the door was worked on "off the books" so to speak, and therefore almost nobody even knew that the work was being done. Including the people who were responsible for checking if it had been done properly.

Boeing management originally blamed Spirit for the mistake because at first glance of the work log Spirit were the only engineers who worked on the door. It was only when they checked a second backchannel work log that they discovered maintenance had been done which required removing the door even though according to the log the door was never removed (the leak is someone at Boeing replaced the rubber seal that sits in between the door and the cabin...).

Yes, someone forgot to insert the bolts however the reality is mistakes happen and telling people not to make mistakes doesn't work. You need to create an environment where mistakes don't get anyone killed and management has failed to do that.

An engineer should not do any work at all unless they have been instructed, in writing, on a well defined schedule, to do that work. And that task should be left open until it has been fully checked to verify it was done properly. That didn't happen here, and apparently it's a regular thing.

Sure, 99.999% of the time those checks are a waste of time. But when you're doing thousands of jobs a day those checks will find problems regularly and that should be all the motivation management needs to make sure the inspections are never skipped.