Wallabies rules state that no guests are allowed in players' rooms, so although the women - one of whom was Ashley-Cooper's sister-in-law.
"There's disappointment (from me), and they are disappointed, too", Cheika said.
"So our leadership group came to me about it earlier in the week and asked me to deal with it in a way I thought appropriate. No third parties are involved, it's just inside of our team", said Cheika. 'This is a situation where two boys brought some friends and family back into their hotel without thinking of the implications of that, because they were friends and family.
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"Be that players on the field, be that support staff, be that any extra support that they think they need to make sure the Wallabies can be in the best place they can be as they move into Japan".
Captain Michael Hooper said players were aware of what happened last week before the Italy game but chose to not tell the coach until early this week.
Cheika, the only coach to have won both the northern and southern hemisphere premier club competitions in 2009 with Leinster in the European Cup and the 2014 Super Rugby title with the Waratahs, said he could not influence that but he had his own strategy in developing better relations with the four Australian Super Rugby franchises.
"It's a minor thing that's in the team code".
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Wallabies skipper Michael Hooper denied there was any disunity in the camp and added: "When we say we're going to put a line in the sand, it's important we stick to that".
"You've got to have the bad bits. They realised their error and they have been trying to help the other players get ready for the game tomorrow [Saturday]", said Cheika.
On Friday, the Wallabies were already reeling from knowing No 8 David Pocock would miss the England game with a neck injury suffered against Italy, when news of Beale and Ashley-Cooper's exclusion became public.
Speaking to reporters earlier in the week, Castle said there would be a usual review process once the Wallabies returned to Australia, with any changes to be made before Christmas.
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Instead, because of the breach, Cheika has been forced to pick two specialist wingers in Sefanaia Naivalu and Marika Koroibete as reserves, leaving their playmaking stocks vulnerable should Matt Toomua or Bernard Foley get injured.