Fuel always comes with samples and a certificate of origin. Also, fuel cargo tanks do not feed directly into machinery. Fuel is pumped from cargo tanks and passes through a centrifuge to the "day tanks", which feed fuel to machinery. A competent engineer would catch contaminated fuel (water, debris, fungus, etc.), as it centrifuges out, and would immediately stop filling the day tanks.
They went dark ship right before the collision => generators. I've had multiple problems in the past where engineers failed to change generator fuel filters. Fortunately none that resulted in incidents (other than me having to change my underwear). Someone(s) combing through the engineers logs and the vessels electronic maintenance system, which can be very telling on the crew and management. Past inspections and audits and any deficiencies (including no sail items if there are any), will be well documented by the classification authority, flag state and shoreside management (management undergoes regular and extensive record keeping audits just like vessels).
Could also have been some nimrod screwing up a generator swap during maintenance (which should have been done at the dock or offshore). I'll bet that investigators already know the cause, or at the very least have strong suspicions.
I'm betting on human error in the engine room with a failed e-gen kicker (more poor maintenance and testing).
https://gcaptain.com/ship-lost-control-before-hitting-baltimore-bridge/
https://www.theautopian.com/heres-everything-we-know-about-the-container-ship-crash-that-destroyed-the-francis-scott-key-bridge-in-baltimore/