When Spock was chasing, and beating, Khan over a transport in San Francisco, Uhura orders them beamed both back to the Enterprise, while Chekov says something like:
Its impossible, they are moving!
But in the first movie, it was Chekov that transported back to Kirk and Sulu, avoiding hitting the Vulcan planet when trying to disable the Romulan drilling platform.
The novelisation gives us a little more info. In short, there's just too much going on for them to get a reliable fix. It's not just that the two fighters are moving, it's that they're on a moving platform moving in and around multiple layers of traffic.
“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.” “Keep trying,” Spock directed the helmsman as he turned.
Sensing a presence at his back, he turned to find himself gazing at Uhura. Their eyes locked. Hers were wet, but her voice was low and thick with anger. “Go get him.”
