The 31-year-old reality star predicted to girlfriend Kaitlynn Carter that there would be trouble between his stepsister and her partner of nine years when pictures emerged of Scott growing close to former girlfriend Chloe Bartoli recently.
He said: "When I saw those pictures I said, 'Uh-oh.'
"I even showed my girlfriend and said, 'This isn't good.' But it's unfortunate."
Though the 'Sex With Brody' star wasn't sure if there had been any signs the couple - who have children Mason, five, Penelope, two, and Reign, six months, together - were on the rocks, he is aware that Scott, whose wild partying and heavy drinking is believed to have contributed to the split, had "some issues".
He added in an interview with 'Today': "Scott and Kourtney both are great.
"Obviously Scott has gone through some issues in the past [but] he has worked through them."
Meanwhile, Brody also spoke of his father's recent gender transition and is "getting to know" Caitlyn Jenner in a "better way" than when she was Bruce.
He said: "Well, growing up, I didn't really have the greatest relationship with Bruce.
"I didn't see him that often. And Caitlyn is just a much freer person. It's incredible to see the difference between Caitlyn and Bruce.
"Bruce and I kind of didn't really get along. And Caitlyn? It's literally like trying to get to know somebody -- like your dad -- over again. But in a better way."
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