The problem was the ship in port had limited crew and limited time to control the fire before it reached a critical size and intensity. Fire while having major life extension and repair is sadly common. I can recall a French SSN having to be repaired following a major fire.
My own personal opinion baked by some friends who served is that the lack of crew made it possible for the fire to reach the intensity it did. Instead of having 900 sailors and officers the complement on hand was minimal. So the reaction time is dismal. The same fire while the ship was underway would be extinguished in minutes.
News reports stated BHR's fire suppression system was offline for maintenance when the fire occurred....