"This is a huge mistake by Kaep," Bowman said on the show with a smile. "I'm sure he understands that now. In his defense, we're young, in our era these days we like to match our snapbacks with our outfits."
49ers teammate Aldon Smith however, took a different view to Kaepernick's choice of cap in an interview Wednesday with ESPN's "First Take," saying, "let's not make this a bigger issue than it has to be."
"He's not in the game, he's not throwing up Miami Dolphins signs," Smith said. "He plays for us, he plays hard for us."
"He can wear a Chicago Bears shirt, it's fine," Smith added. "As long as he's dedicated to what he does and he does a great job on the field and he's dedicated to his team and he's a leader for us, that's all that matters."
On July 5, he responded to backlash on social media by posting a photo on Instagram of him holding the Dolphins cap with a smirk, asking, "This the hat y'all mad at?"
"I'm goin wear what I want regardless of what you think, all you need to worry about is the fact that I grind for my teammates and the 49ers! I plan on doin this until they won't let me in the building!" he wrote, adding hashtags of #ridiculous and #y'allmustbebored.
Just three days later, however, he tried to make amends after backlash from fans and the media by posing in an Instagram photo wearing a 49ers cap and writing, "It's just swag it ain't never hurt nobody!"
Bowman's advice to Kaepernick for the future is to stick to wearing caps of teams in other sports leagues.
"The hats now these days are very important to the outfit, so Kaep, I understand what you did, but let's stay away from the NFL teams. Stick to NBA, go to college or the baseball hats," he said on the show.
Smith, however, doesn't agree that Kaepernick has to stay away from NFL gear other than the 49ers'.
"When Colin rushes for 1,500 yards, it doesn't matter," Smith said. "He can wear the team that he ran the yards on. Let him have fun."