The 36-year-old rapper, who is married to pregnant 35-year-old Kourtney's sister Kim, 33, allegedly doesn't agree with Scott's continuous partying.
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According to sources, Kanye, who has one-year-old daughter North with Kim, can't understand why Scott, 31, wouldn't want to be at home with his pregnant wife and children - Mason, 4, and two-year-old Penelope.
An insider told a US website: "Kanye would never leave Kim when she was pregnant, unless it was to bring money back home to the family.
"Big money. He didn't leave Kim alone when she was pregnant unless he was clocking six figures."
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When Kim was six-months pregnant with North, Kanye was based in Paris recording new music while Kim was living in LA.
But Kanye apparently believes "when she's pregnant, guess what - you're pregnant too", and thinks Scott is a "hot, toxic mess" who is "partying like the world is going to end".
Scott has been dealing with the deaths of his parents this year. His mother Bonnie died in October last year, followed by his dad Jeffrey in January.
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He and Kourtney have already faced problems with his drinking recently, with her telling him to quit the booze or leave their home during a recent episode of Keeping Up With a The Kardashians.
She raged: "Unless you want to be sober, then I don't want you here. If you want to die then you can continue to act this way."
Kourtney and Scott have been together since 2006, after meeting at a friend's party.