AndyO. wrote:

I don't see anything weird about Sherlock catching the pen xD He knew John was going to throw it and he also saw it (even if not looking directly at the pen). It's not that hard to catch things.

 
It's a bit odd that Sherlock catch the pen with his left hand, I think for a right handed person it is not that easy to  catch something this way. This remind to the scene as Sherlock plays with the rubber ball in the Labor  (TRF), it seemed to me that he trained the reflex of his left hand.