The charges relate to the U's game against Blackpool last weekend in which Fagan was used as a second half substitute during the 1-1 draw at Bloomfield Road.
Ironically, Fagan wasn't cautioned by the match official during that game.
The former Blues striker is clearly finding his feet at Layer Road scoring six times in the U's opening twelve games this term but his disciplinary record fails to improve by the look of things. He has already received six yellow cards so far this season.
Last season Fagan received 13 yellow cards and 2 reds in his first season with the League One side.