In Days of Future Past, Quicksilver holds Magneto's head to prevent whiplash. However, in Apocalypse, Quicksilver not only ignores holding heads (not everyone), he also throws people. Did they make a movie mistake, or is there some explanation of this?
In Days of Future Past, Quicksilver was trying to get one important guy out of jail. Key aims: keep Magneto safe, and get him out in the few minutes before the whole place is on lockdown.
In Apocalypse, Quicksilver was trying to get every student out of an already-exploding school. Key aims: get everyone away from the explosion in the one or two seconds before it engulfs and certainly kills them.
As such, he doesn’t have time to hold everyone’s head. More risk of injury for any given individual is acceptable, given that the alternative is immediate firey death, and he’s got a lot of kids he wants to save in a very short period of time. As you'll notice, some kids he just literally throws out onto the ground.
Sorry! No movie mistake for you today!
I can't remember him doing that in the film. But it may be, as someone has already suggested, that he was playing it safe. It may be important to note that Magneto is Quicksilvers father. This is alluded to in DoFP and confirmed in Apocalypse. This may be why he was more cautious with Magneto than he was with others.