On balance, I think it’s more likely to be caused by sabotage by the crew.
It makes no sense to continue to lie about the carrier being hit if that’s what happened, as that’s not something you can cover up in the long term, so when the truth inevitably comes out, the cover up is going to look worse than the original event. Once the ship pulls up in Crete or any other dock, a hit by weapons would be obvious for all to see.
The odds of a missile or drone strike against a carrier not resulting in any casualties amongst the crew also seems like a very low probability event. Especially since at that distance, it’s almost certainly going to be a ballistic missile or proper AShM and not some FPV with minimal warhead.
Otoh, a fire originated in a non-critical part of the ship (so no guards, access controls or permanent personnel presence), that just so happens to take out hundreds of berths forcing the ship to return to port seems like exactly the kind of Hail Mary play a disgruntled crew desperate to go home would think to do. So the spread of the fire would likely be deliberately engineered, possibly with accelerants, maybe also with targeted sabotage of key fire fighting and damage control equipment in the vicinity to frustrate initial response, or wilfully incompetent performance from damage control parties, or maybe a combination of some or all of the above. This seems like the far more likely cause.
Although with the track record of Trump blatantly trying to gaslight everyone thus far, I would not be surprised if the Ford does pull in with 600 bedsheets stitched together to cover a large section of the ship.