Jenner said in a since-deleted post on Instagram Stories she thought the stunt by YouTube user Christian Adam went too far.
"Idk if this is really a social experiment to some people but you're messing with real people, real relationships, real family," she wrote.
"I'm happy my relationship is strong because this is getting out of hand. The internet scares me sometimes for real."
Jenner's sister Kim Kardashian also called out Adam in a tweet Wednesday, saying the prank was "absolutely disgusting."
"I hate that I am bringing attention to this but this is absolutely disgusting that you would find this funny to mess with Travis & Kylie who just started a family together. This is really damaging to relationships, families and is just so wrong!" she wrote.
Adam confirmed in a video Wednesday he faked the photo of Scott by dyeing his hair to better resemble the rapper.
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He explained he meant for the prank to show how "gullible" the Internet is.
"DISCLAIMER: this video was NOT made to intentionally hurt Travis Scott, Kylie Jenner or the entire Kardashian family in ANY way shape or form," Adam captioned the post.
Scott denied cheating on Jenner after the photo surfaced Monday.
The couple started dating in April 2017 and welcomed their first child, daughter Stormi, in February.
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