Watson is unhappy he wasn't involved in hiring new general manager Nick Caserio after team owner Cal McNair told the 25-year-old he would be a part of the decision, sources told NFL Network's Ian Rapoport reports.
Watson offered his input on general manager candidates, but the team didn't consult or consider those names before hiring the former New England Patriots executive, ESPN's Adam Schefter reports, citing league sources.
The Texans didn't tell Watson they were going to hire Caserio, and he learned of the move through social media, Schefter adds.
That prompted Watson to tweet, "Some things never change." He later deleted the message.
The team hasn't heard from its star player in the last few days, though it attempted to contact him, according to Rapoport.
In addition, Watson advocated for the team to pursue Kansas City Chiefs offensive coordinator Eric Bieniemy for its head-coaching vacancy, reports Albert Breer of The MMQB. However, the Texans are the only team with a head-coach opening to not request an interview with Bieniemy.
Watson has been vocal about his desire for change within the Texans organization.
"We just need a whole culture shift," he said after the team's final regular-season game.
"We just need new energy. We just need discipline. We need structure. We need a leader so we can follow that leader as players. That's what we need," he added. "We've all got to be on the same page. There's too many different minds, too many different ideas, and too many people thinking they have this power, and it's not like that."
Caserio wasn't on a list of GM candidates recommended to the Texans by a search firm, according to NFL Network's Mike Garafolo.
This follows a series of questionable moves by the franchise, including the surprise trade of superstar receiver DeAndre Hopkins to the Arizona Cardinals in the offseason.
Watson led the NFL with 4,823 passing yards this season, despite Houston's 4-12 record.
He signed a four-year, $156-million extension with the Texans in September.
Watson hasn't requested a trade and his contract includes a no-trade clause, according to Aaron Wilson of the Houston Chronicle.