The novelisation indicates that he's moving too fast and that the abundance of other life-signals in the area is making it impossible to track him long enough to beam him out (as well as moving through buildings laced with materials that make it difficult to get a lock).
Another pause, followed by a startled exclamation from Sulu. “Got something. One life-form.” He looked back at Spock. “Whoa—he just jumped thirty feet!”
“That’s him,” Spock declared with confidence. “Can we beam him up?”
Try as he might to make it possible, in the crowded confines of the compound and the city below, the effort required exceeded even Sulu’s exceptional skills.
“He’s moving too fast, and there are too many other people around. I can’t get a lock on him.”
Chekov studied his instrumentation. “I think they’re on a transport of
some kind. They keep moving too fast in and out of structural
surroundings filled with people to still be on foot. I can’t get a
lock on either of them.”
One assumes that they were beamed off once the hover-thingy reached its destination or once the driver realised that there were people having a climactic battle on his roof and slowed down.