The 49ers posted dozens of photos on their website of past games against the Packers before the teams meet again Monday night, but at first did not include any of Kaepernick.
The team later added photos of Kaepernick. This is the first photo gallery the 49ers have run this year; pictures of Kaepernick were included in all seven galleries posted on the team's website last year.
"Unfortunately there were a handful of obvious misses in this gallery posted by our website team and we appreciate them being brought to our attention," the 49ers said in a statement. "The 49ers organization has tremendous respect and gratitude for the contributions Colin made to our team over the years."
Kaepernick set an NFL record for quarterbacks by rushing for 181 yards in a playoff win over Green Bay on Jan. 12, 2013; threw for 413 yards in a season-opening win against the Packers in 2013; and led a winning drive in a playoff game in Green Bay on Jan. 5, 2014.
"We have fond memories of those games and that should have been displayed on our website," the team said. "This oversight does not properly reflect the appreciation our ownership and this team have for Colin."
The 49ers supported Kaepernick in 2016 when he decided to kneel during the national anthem to protest social and racial injustice and matched his $1 million contribution toward programs for social equality.
Kaepernick opted out of his contract the next offseason when the 49ers told him they planned to cut him. Kaepernick has been unable to find another team to play for the past two seasons.
Coach Kyle Shanahan was asked about bringing Kaepernick back after starting quarterback Jimmy Garoppolo went down with a season-ending knee injury, but said Kaepernick didn't fit the team's offense.
"I made that decision just with the style of offense that we wanted to go with," Shanahan said Sept. 24. "That's kind of what I said last year, and it's kind of the same situation now. ... I always look into what style of offense I want to do, what style of offense we've been doing for the last two years."