The bolts were installed by the contractor, but had been installed incorrectly. The old bolts were then taken out at Boeing but no one thought to install the new ones.
This one was a twofer according to the preliminary report. There were 5 bad rivets near the door frame that had to be replaced. This happened at Spirit Areosystems. The door plug was removed to do the work at Boeing. The bolts were never put back in.