It only has the one f-bomb. If it uses more than one, it gets an R-rating. But it has fair amount of swearing beyond that one f-word, which still pushes the limits of the PG-13 rating.
As Nell also just pointed out, it has some of the most violent sequences seen in the X-Men films so far, from Logan's burns from the atom bomb, to the various stabbings, shootings, poisonings, and fight scenes, and of course the scene where Logan claws his way to his own heart to get the nano-bug out.
What's interesting is that I read that they were able to get away with the heart surgery scene because according to MPAA rules, Logan being a mutant means he's not human, so it didn't count the same way.
And, even though we don't see it, it's pretty obvious that Logan and Mariko spent the night together, and that adds to the content counted towards the PG-13 as well.
So while what we end up seeing in this missing ninja fight may or not be so explicit on its own for an R-rating, you have to consider everything else that contributed to the movie's rating.