A section of supporters within the stadium jeered loudly as players from both teams linked arms before kick-off for what the league had described as "a moment of silence dedicated to the ongoing fight for equality in our country".
"How can you be more upset about bringing awareness to racism than racism itself?" Baltimore Ravens quarterback Robert Griffin III wrote on Twitter.
Fewer than a quarter of the stadium's seats were occupied due to COVID-19 restrictions but a scatter of boos mixed into cheers were audible to Texans' defensive end J.J. Watt.
"I don't fully understand that, there was no flag involved," he said. "There was nothing involved other than two teams coming together to show unity."
Chiefs quarterback Patrick Mahomes acknowledged seeing videos of interruptions to the pre-game demonstration, which he had helped organise with Texans quarterback Deshaun Watson during the week.
"Being down there, I honestly didn't hear a lot of booing. I've seen a little bit of the video after," Mahomes told reporters.
"I'm just -- we wanted to show unity and we wanted to show we're going to come together and fight the good fight."
Both head coaches said they did not hear the jeers but Texans coach Bill O'Brien suggested the boos may have been for the visiting team.
"Maybe they were just booing us because we had just come on the field," O'Brien said. "But yeah, I thought that that (the moment of silence) was a very nice gesture."
Kansas City councilman Eric Bunch said the fans who booed proved their protests had nothing to do with disrespect for the American flag.
"Some NFL fans booing the players for standing and locking arms in a moment of silent for unity proves that for them the 'standing for the flag' was always about perpetuating white supremacy," Bunch wrote on Twitter.
(Reporting by Hardik Vyas and Rohith Nair in Bengaluru; Editing by Ken Ferris)