Ultimately, Mangold decided that the actual demise of the mutant super-team should take place off-screen in Logan the movie, but as he explained to me, the slaughter of the X-Men was originally intended to be shown on the big screen as well.
“I literally had written an opening which started with that sequence,” said Mangold. “And so it was quite literal, who was dead. But the reason we didn't do it wasn't to spare other films, it was that it redefined the movie. It made the movie about the X-Men, instead of being about Logan and Charles. And irrevocably, when you read the script opening that way, it became about this other tragedy, as opposed to that tragedy being something hovering like a shadow in the background for these characters.”
In the film, we do hear a radio report indicating that several of the X-Men were killed in an incident in Westchester, New York (home of the X-Mansion), but Mangold says he had a pretty good idea as to which of the members actually went down. In the end though he decided it was best not to “nail it down” so precisely.
Of course, in the Old Man Logan comics the death of the X-Men was brutally depicted. Whereas in the film we learn that Xavier had inadvertently killed his own students due to a degenerative brain disorder that caused him to lose control of his telepathic powers, in the comic Logan himself committed the heinous deed.