A number of years ago an aircraft carrier, the Oriskany, was sunk off the coast of Florida. It was (and is) against the law to remove anything from the wreck. Soon after it was sunk, a diver removed a large control panel (IIRC) from the wreck, and he wrote about doing so on the Internet. Asked about it, the skipper of the boat said that he could not control what divers did when they were underwater. He did not know it had happened. Unfortunately for that defense, when the diver wrote about it, he thanked the skipper for his help in telling him where to find the control panel and helping him bring it back on board. (Remember that it was big--hard to miss.) After the ensuing uproar, the diver apparently returned it to its rightful place. Soon after, someone else managed to take it and get it back on board an operator's boat without anyone noticing it, and this time the diver was wise enough not to brag about it publicly.
I was on a boat in Cozumel a couple of years ago on which a diver was pulling on his gloves and preparing his goody bag for all the souvenirs he was planning to bring to the surface. Neither the skipper nor the DM said a word. Before he splashed, I told him that both wearing gloves and bringing anything up from the marine park were against the law there. He did not know that, so he took the gloves off and stowed the goody bag.
I dived with an operator in Belize that had a clearly written policy prohibiting the use of gloves on dives. On one dive I saw a family of three all wearing gloves, and I saw why--they used them to pull themselves along the living reef continually as they dived. After that dive, I spoke to the DM about it, and he assured me he would take care of it. They did it again on the next dive, without a hint of disapproval from the DM.
The Mike Ball company in Australia has a strict policy requiring all divers to take a checkout dive before diving the Great Barrier Reef with them. They allowed Gabe and Tina Watson to skip that required checkout dive despite the fact that it was Tina's first ocean dive and first dive after OW certification, simply because Gabe, a relatively inexperienced ocean diver himself, said they didn't need it because he had rescue diver certification. Mike Ball paid a hefty fine for violating their own policies when Tina died and Gabe was unable to save her.
Go to the Cozumel forum and see how many threads talk about regular customers of dive operators being allowed to do bounce dives to 200 feet while the rest of the group follows the DM above them, a clear violation of Cozumel law and operator policy.
I am sure that the overwhelming majority of dive operators strictly follow all policies and all laws with all customers, but it is perfectly clear that some do not. I am not saying that it happened in this case. I am not saying that news articles are 100% accurate--in fact, that would be rare. I am simply saying that the news article suggests that the boat crew did know what they were doing, and it is possible--however unlikely that it may be--that in this case it was accurate.