I've never seen a clue not given to a team for a transportation mistake mid-leg. Hell, we've had teams miss clues and have to go back to get them and no one told them to go back.
Not many clues get handed out by actual human beings, though - I think they're fairly consistent that whenever there's Phil, or in this a local, at a checkpoint, they'll stop them if they've made a mistake. If there's just clueboxes, they can't do anything to regulate it.