The 23-year-old full-back has been one of Leeds's standout players so far this season, with his form seeing him linked to a number of Premier League clubs ahead of the summer transfer window.
Taylor now appears to be trying to push through a move, but Monk warned that the club will take a "strong stance" against the player following his actions.
"There's no sugar-coating this - Charlie refused to play the game. I think he's been terribly advised...I think he's been poorly advised all season. We've tried to guide him and help him. He's a young lad, a good lad, but he's a bit naive," he told reporters.
"To refuse to play the game, for me as a manager and for the club, that's unacceptable. I've got a lot of time for Charlie, as we all have at the club. He's not very experienced in these situations, and you need proper guidance, and people around you who can help you do things right.
"He'll learn from this but, as a manager and a club, you cannot have a player refusing to play. The club will have a strong stance on this, I'm sure."
Leeds went on to draw 1-1 with Wigan to finish the season in seventh place, five points adrift of the playoffs.