This is considered a "blocked ball," and we have to ask ourselves: who created the blocked ball, the offense or defense (ie., who's out of the dugout that shouldn't be)?
If the defense created the blocked ball, then it's handled the same as an overthrow. All runners are awarded 2 bases from their position at the time of the throw.
If the offense created the blocked ball, then the ball becomes immediately dead, and all runners return to the last base(s) they touched. If the blocked ball hindered the defense from making a play on a runner, then that runner is declared out. However, the umpire must judge that the defense had a reasonable chance at getting that runner out. If they'd already crossed the plate, are standing on a base, the throw was way off, etc., then it's just a dead ball.