Personally, I consider phases to be the broad categories: offense, defense, special teams.
I don't think its controversial to say that is the generally accepted understanding of the meaning of that phrase:
http://bleacherreport.com/articles/2300656-patriots-winning-in-all-three-phases-of-the-game
Penalizes are subsumed within those categories or phases. Obviously they are important.
Semantics I suppose, but that's the way I've generally heard the phrase used.
So I do think there has been improvement across the board - in every phase of the game.
Edited by MUTGR at 15:12:52 on 11/19/17