In the fight scene in the Buy More with Shaw, Chuck gets hit and pushes the Jeffster DVD into the DVD player. After it's in and already playing, the camera cuts to a side view of Chuck and the tray of the DVD player is still closing.
After the final fight with Shaw, Sarah gives Chuck the governor and they hug. During the hug, between shots, their arms change position.
Since Shaw now has the intersect he would flash on Chuck wearing fake beard and figure out who he is quickly.