Make sure you have your team practices fouling in late game situations when you want to stop the clock with the other team leading and they have the ball.
Practice having your players go after the ball and try to steal it from the dribbler or the player holding the ball. If they do not get a clean steal then they should make some body contact to draw the foul and stop the clock.
By doing this you should not get an intentional foul called if you tried to play the ball, not the player with the ball.
However, you have to practice these situations. Put time/score uon the clock in different situations of time and score. This will pay off in the long run and could prevent intentional fouls being called late in the game when you want to stop the clock because you are behind.