See, there's a reason why Marvel Studios has a guy like Kevin Feige at the top to make sure everything fits correctly.
The last two X-Men-related films shared a character, but it definitely wasn't part of a larger plan or franchise synergy. No, it was mostly just a lack of communication. Oops.
Director James Mangold was asked about his use of the character Caliban in Logan as well as the character's appearance in X-Men: Apocalypse. For those keeping score, the films took place 46 years apart, with Caliban played by Stephen Merchant in Logan and Tómas Lemarquis in Apocalypse. Mangold told Nerdist the character wound up in both movies because there wasn't really a lot of communication between the two camps and the character was just randomly written into both films.
Here's an excerpt from how he explained it to Nerdist:
"It's a funny, messy story of how so often these things are not as coordinated as everyone thinks. I actually had written him into our movie, and they didn't know [he was] in Apocalypse, and then they kind of wrote it in their movie, and they cast someone in their movie and I had not seen it and was working away on mine."
Once he became aware of the double-booking during production, Mangold decided to leave the character in because he didn't want to compromise his story to make it fit better with another movie.