All of the comic covers were made specifically for the movie.
According to this interview with director James Mangold at Slashfilm,
Logan also incorporates the idea of X-Men comics in a really interesting way. So first of all, how many of those comics are actual comics that exist, and then how many did you make up? And second, how did the idea come to you?
We had to make them all. Marvel only agreed to let me do this as long as we didn’t use any real Marvel comics. So we made them all up. But they involved existing Marvel characters. But they just couldn’t be real Marvel comics. You’d have to go ask Marvel why.
Another article on The Verge reveals the covers were created by artist Dan Panosian with some interior art by Joe Quesada, and has quotes from Panosian on the assignment:
In all, Panosian created 10 fake covers for the comics used in the film, while “Joe Quesada penciled four pages that I inked / colored and lettered that you see featured throughout the film.”
He received open-ended directions on what the covers should look like. “The themes were easy to select,” he noted, because the films covered many of the same elements as the stories that he had grown up reading.