A 44th-minute own goal from Jamal Fyfield and substitute Nick Chadwick's late strike condemned the Minstermen to their second defeat in three matches.
The York boss said: "We were second best to everything from start to finish. They were winning more second balls virtually for the 90 minutes, obviously that was disappointing.
"If you are not going to win second balls and are second best to everything, like we were, then we are going to end up losing games.
"Plymouth thoroughly deserved the three points and we got what we got: absolutely nothing. It's basic. We passed the ball very well last week but we got the ball in the first place to enable us to play.
"Today (Saturday) was totally different, they were in our faces from the word go and didn't allow us to pass the ball and when it's like that you sometimes have to hook the ball on and put their back four under pressure.
"My back four were under pressure for 90 minutes because we didn't do that. It's not complicated, it's simple. We have to be better than we were just by anticipating where that ball is going to be and getting their first. We were second to it."