"I think Dale doesn't like me and he's running the show," Stewart tweeted. "... there [sic] going to let me rott [sic] in AAA all season and then non tender me after."
Following Iowa's game on Tuesday, Stewart sent out three tweets apologizing for his remarks.
"I let my frustrations get the best of me and in no way want to be a distraction," he tweeted Tuesday.
He also tweeted that he was working every day to make it back to the Major Leagues.
Stewart is signed to a one-year, $2 million contract with Chicago.
Chris Iseman is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.