It's possible, at least in the movie-universe" a degree or two of "will" on Shaw's part has to take place in order to absorb energy much like Magneto has to use a degree or two of "will" to use his "magnetism" powers, he doesn't just attract all metal everywhere and anywhere whether he wants to or not. He has to make a decision and even exert some form of effort (either physically, mentally or both) to manipulate metals.
Shaw could be the same way, he doesn't absorb all energy everywhere and anywhere no matter what he has to want to absorb it and exert some kind of effort to do so. Now, as Magneto has gotten more adept at using his powers over the years from manipulating metals almost randomly during times of emotional outburst, to being able to manipulate small metal objects at will to being able to lift submarines out of the sea, Shaw also has learned to absorb energy almost without thought or "trying" but it still requires some-kind-of thought on his part to do it.
Since Xavier had Shaw under his control during the scene it's possible Shaw could no longer exert any will on his powers so he was pretty much vulnerable to the coin's kinetic energy. (Much like how we see Mystique revert back to her "true form" after being knocked out in X1 or similar times in the movies where someone is knocked out and and their powers stop working.) Hell, the only person I can think of off-hand whose powers don't require "will" is Wolverine whose powers seem to not be an at-will one but just a very-advanced form of a natural biological process. (Thus, Wolverine heals even when knocked out.)
Yea, that's the way I took the scene, Shaw has to actively engage his power, and while Erik was actively engaging Shaw from the front, with attacks he fought off, Erik, slipped through the back door with the coin Shaw didn't see coming, and didn't have a chance to defend himself against.
One Day I hope to be the Man my Cat thinks I am
Where are we going? And why are we in this Handbasket?