"As long as Shady's talking, he's fine," Incognito said.
Buffalo fans greeted Kaepernick roughly for his leadership among athletes protesting during the national anthem. They booed him loudly, sold anti-Kaepernick T-shirts and roughed up a dummy wearing his jersey.
"I thought he was OK," coach Chip Kelly said of Kaepernick, whom he promoted over Blaine Gabbert following a 33-21 loss to Arizona. "But overall, offensively as a group, we need to run the ball better and we need to be better at the passing game."
Kelly wouldn't commit to who will start next week against Tampa Bay.
"Yeah, we'll see," he said.
Tyrod Taylor threw two touchdown passes in helping Buffalo win four straight for the first time since the start of the 2008 season.
The 49ers allowed 312 yards rushing - Buffalo's best outing since 1992. The defense has allowed 981 yards on the ground in its past five games.
The Bills blew the game open by scoring 21 points over a span of 7:02 straddling the third and fourth quarters.
McCoy scored twice on 18-yard runs and another on a 4-yard scamper in his second meeting against Kelly. McCoy expressed bitter feelings toward Kelly for trading him from Philadelphia to Buffalo.
"To sit here and tell you that it didn't affect me last year, I would be lying," McCoy said. "But I'm past that. It's a whole year later."
Copyright 2016 by The Associated Press