This is the latest twist at the intersection of politics, sports and music that has surrounded this year’s Super Bowl. Kaepernick is still in the middle of an ongoing arbitration case regarding a grievance he filed against the N.F.L. He has accused the league’s owners of colluding to keep him out of the league after not being signed last season.

His protests during the anthems became a cultural flash point, even though he wasn’t in the league. Other N.F.L. players began kneeling to support Kaepernick, as did celebrities off the field. Last fall, Nike made Kaepernick the face of a prominent advertising campaign.

This year’s Super Bowl became particularly fraught because of the halftime show. Some high-profile artists, including the rapper Cardi B, said they would not be willing to perform, in a show of solidarity with Kaepernick. Last year, Jay-Z rapped in one of his songs: “I said no to the Super Bowl, you need me, I don’t need you.”

Earlier this week, the N.F.L. announced the halftime acts would be Maroon 5 and the rappers Travis Scott and Big Boi. Scott’s decision to participate, in particular, received backlash, including from prominent African-Americans like Al Sharpton. Variety reported that Kaepernick and Scott spoke before the announcement and described the conversation as “cordial and respectful.” But on Wednesday, several posts critical of Scott appeared on Kaepernick’s Twitter account.