Juggernaut was supposed to be a mutant as Leech's powers worked on him, and Magneto calls him a "brother"during the rescue. More than likely they didn't want to waste screen time explaining that Juggy's powers came from an other-dimensional god, or how he came to be granted them.
The Sentinels may have been robots, but they gained their powers (somehow) from a mutant (Mystique), while in Logan they couldn't very well say no new mutants had been born in a while, and then have mutants hunting the heroes. Besides, it would negate the whole need for chasing down the escaped mutant children if they already had mutants working for them.

I'm hoping an AF movie will expand to include other means for the heroes to have powers (i.e.: magic, science, divinity) so as to maybe connect to the FFCU where there seemed to be no mutants. That way Fox could maybe have characters crossover between films like in the MCU.