I figured out the skip-stop. I looked at the Subway map more closely. The skips different stops than the and vise-versa.
Why can't they do this in other parts of the subway? They should do skip-stop on the Brighton line () as well. Avenue M is a popular stop but if you wait for the at Newkirk Plaza, once you wait for the train to come, the train is already passed Prospect Park resulting in it not worth waiting for the at Newkirk Plaza and staying on the .