He did the same thing when he helped Magneto escape from the Pentagon in First Class.
I figure he probably did it with the kids he rescued from the school earlier (oh, there's that song in my head again), but the camera angle was facing them so we didn't see it.
I assumed the MIB agent was wearing a bulletproof vest under his suit or something, but still getting hit by a bullet would knock you down. Better than getting a full on punch from Barry, and we know what happened last time Barry punched someone.
I hadn't thought about the vest possibility -- that would be preferable to Barry suddenly deciding to kill some guy as a cute stunt, though it still seems like kind of a jerk move.
But in fact, getting hit by a bullet would
not knock you down. The Mythbusters debunked that twice, and you can find YouTube videos debunking it too. A bullet just doesn't have enough kinetic energy to impart more force to the body than the equivalent of a mild shove. And any experienced hunter will tell you that animals who get shot will more likely run away than fall over, unless you happen to hit a vital area. The reasons why people fall down when shot
are unclear, but it's probably due to the pain and concussive shock glitching the nervous system, or even due to a conditioned psychological reflex to fall down so as to present less of a target.
Unsurprisingly, even fiction is quite inconsistent about this. A lot of action scenes assume that getting hit by a bullet with fling a person backward as much as several yards, depending on the absurdity (though the shooter is never thrown back with equivalent force as Newton's Third Law would demand), but there are also tropes that depend on characters
not being knocked down by bullets -- like the trope of characters thinking they're fine and only gradually realizing they've been shot, or the trope where two people are wrestling over a gun that goes off and they both stay standing for several moments before one falls dead.
To go back to
X-Men: Apocalypse, there was Wolverine's cameo where he was shot many times and didn't get knocked down. And he only has a healing factor, not superstrength. If bullets did knock people over, he would've been knocked over.