As a seasoned veteran of Yankee stadium I can say the wave breaks out pretty much every night game (excluding boston and the mets). However I have never seen it occur outside of the upperdeck and the left field bleachers.
I am not sure where you were sitting, but the most fascinating place to sit is the right field bleachers with the bleacher creatures. They have a song for anything that occurs, including a 5 minute ballad called "at the gangbang". Roll Call is also pretty cool to see.