The 17-year-old's father Bruce, 65, recently made the brave decision to debut as a woman on the cover of Vanity Fair, asking to be called Caitlyn from now on.
While Caitlyn has been inundated with praise for the move, it seems singer Chris, 26, isn't a fan.
He reposted a meme from rapper Snoop Dogg with the message: "Shout out to Akon ! He is about to supply 600 million Africans with solar power. Im really upset that this isnt major news but that science project bruce jenner is #Society [sic]."
Chris swiftly removed the post, after huge backlash from his followers, but not before some fans screen grabbed what appeared to be a reply from Kylie's official Instagram.
She allegedly wrote: "Not very nice thing to say about your friends dad [sic]."
Kylie then tweeted: "State what you want about the world without bashing others. Leave a positive impact."
Chris' decision to repost the transphobic message came as a shock to some, as he is close friends with Kylie and her sister Kendall, 19, and her rumoured boyfriend Tyga.