In all cases, there is a more or less direct implication that the player(s) lack the skill or integrity to deserve a place in the game.
A clean route is a path which takes the runner away from potential tacklers and into space where the thrown ball can be received.
Since a Hail Mary play involves almost all offensive players being runners, this would imply the offensive players are either unable to run into such space or actively run into defensive players.
"In a dome" implies an indoor field, which almost always use artificial turf due to the difficulty of maintaining real grass. Artificial turf does not require dirt, does not become more than damp, and therefore should never be muddy.
"Have/Got game" is a term describing general prowess in more than just pure playing skill, but in the meta aspects of the sport.
This suggests the player added mud to their jersey, attempting to appear committed to the game (since the mud would come from being tackled or blocked, evidence of being active in play) but ironically forgetting there should be no mud regardless.
A flag thrown "on" a player implies the player had committed a foul which resulted in a flag being thrown by a referee or other official such as an illegitimate interference with a pass, thereby preventing a good offensive play.
Since the quarterback is the one making the pass, this suggests they are somehow interfering with their own team's intent, further implying a lack of throwing skill or perhaps even sabotage and cheating of some kind.