The whole issue appears to be that they did not formally announce that it was a problem. This seems more like an internal NASA political issue, than a real one.
Well, yes, and no. Not declaring it a formal safety issue also meant that the full force of the NASA resources across all divisions were not brought to bear at the time, and that would also mean that next steps would need to be formally coordinated with high levels of consensus as to those next steps. NASA, like many such large organizations, has a lot of groups that are the best of the best of the best in their field, but might not realize that other alternatives and approaches might be more appropriate. It would also have added a level of bureaucracy that many groups don't want to work under, but sometimes, that really is the best answer. NASA (and Boeing) dodged a bullet and did not lose the crew or the craft, but they came a lot closer than they should have to such a disaster (space is hard, every flight has a probability of loss of mission, but NASA needs that number to be very low, especially for missions involving humans).