Yes. That head-counting method the staff guy used was sloppy and shoddy. They should have a register with the names of everyone on the dive listed. Then do a roll call before starting back. That way, you can make sure everyone is accounted for. I'm sure that's the way they do it now on these shore excursions, but at the the Lonegrins, the couple in real life who were the basis for the movie, made their fateful dive, the method of keeping track was probably as slip-shot as the one in the film. The company that lost the Lonegrins had to pay out a huge damage award to the couple's next of kin, and subsequently went out of business.
As you noted, everything that happens to the movie couple after the ship left them behind is the speculation of Chris Kentis, who wrote the screenplay, but it may have gone down very much like that. It must've been very horrible for them, the poor people.

Its definitely 100% the diving company's fault. How could it not be?

But do we REALLY know what occurred that resulted in them being left behind? Unless you are just going by the movie, it can't be certain that they spent more time diving than they were supposed to so I think it's unfair that you blame them for what happened. In all honesty, I place 100% of the blame on the diving company for leaving them behind. If they bring people out there, they'd better make sure they bring them all back.
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Lance Henriksen is KING!
RIP MASK!

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Went was he always chasing the skipper instead of Mary Ann? Makes ya wonder

That's how I felt about Gilligan.