Running a 'tight ship' is great when you have a budget to burn on excellent quality crew. But shipping is so incredibly cut-throat that the crew members make very little money, are effectively modern slaves and tend to carry responsibilities way above their pay grade. They did what they could, and more than that, and for their efforts they were rewarded with what effectively amounted to house arrest while the authorities did their thing. The NTSB of course will focus on the 'hard' causes. But you can see a lot of frustration shine through towards the owners who even in light of the preliminary findings had changed absolutely nothing on the rest of their fleet.
The recommendation to inspect the whole ship with an IR camera had me laughing out loud. We're talking about a couple of kilometers of poorly accessible duct work and cabinets. You can do that while in port, but while you're in port most systems are idle or near idle and so you won't ever find an issue like this until you are underway, when vibration goes up and power consumption shoots up compared to being in port.
There is no shipping company that is effectively going to do a sea trial after every minor repair, usually there is a technician from some supplier that boards the vessel (often while it is underway), makes some fix and then goes off-board again. Vessels that are not moving are money sinks so the goal is to keep turnaround time in port to an absolute minimum.
What should really amaze you is how few of these incidents there are. In spite of this being a regulated industry it is first and foremost an oversight failure, if the regulators would have more budget and more manpower there maybe would be a stronger drive to get things technically in good order (resist temptation: 'shipshape').