The umpire behind the plate knew the girl was illegal.
I'd be interested to know how he knew.
Umpires do not get copies of team rosters and they do not personally check I.D.'s or birth certificates. Generally, they have no way to to verify a player is who she says she is or if the player is even on the roster.
Now, there may have been rumors floating around about this player and maybe the umpire heard them. That still doesn't mean that he "knows", 100% certain for a fact, who the player really is or if she is a rostered, eligible player.
An umpire is in a poor position to make an on-the-spot determination about a player's eligibility because he really doesn't have anything to go by. If brought to his attention he may make a note of it, accepting that as an official protest and then continuing the game. He may even get the TD involved before continuing. But the final determination on roster issues rests solely with the TD and until you get him involved there really isn't much that can be done to fix this.