Police made 11 arrests after trouble flared between both sets of fans before and after the goalless draw at Loftus Road.
But Ambler told Sky Sports News: "We are really disappointed that Millwall's name is associated with these incidents outside the ground.
"I'm thankful these incidents are relatively rare. To put it in context the same supporters went to Cardiff on Saturday and were praised by the police.
"I feel sorry for the loyal Millwall fans who have to put up with this away from home. They are normally very well behaved.