Yes, it appears the 49ers were so furious with Kaep that they went after Matthews instead of their own teammate
which might have something to do with the fact he had told ESPN before the game he would target Kaep to give him as many hits as possible:
http://bleacherreport.com/articles/1766330-clay-matthews-hit-on-colin-kaepernick-leads-to-packers-49ers-fight
The 49ers had a third-down play deep in Green Bay territory in the second quarter, and Kaepernick scrambled to his left in an effort to get the first down. While he went out of bounds short of the marker, Clay Matthews didn't let up on the play.
After Kaepernick stepped out of bounds, the Packers linebacker brought him down to the ground hard:
This led to a fight between the two sides
as several 49ers players came in to protect their quarterback:
San Francisco offensive lineman Joe Staley was the first to grab Matthews and in turn received a 15-yard unsportsmanlike conduct penalty. This offset the 15-yard penalty by Green Bay for a late hit.
The teams then replayed the down, which resulted in a 10-yard touchdown pass to Anquan Boldin.
Former NFL vice president of officiating Mike Pereira believes the refs blew the call:
One concerning part of the play was the fact Matthews appears to have planned this coming into the game. According to Vinnie Iyer of Sporting News, the veteran player told ESPN's Mike and Mike that his team will try to put as many hits on Kaepernick as possible.
This led to some concern from San Francisco coach Jim Harbaugh, who was afraid that the Packers were going to target his quarterback, as relayed by ESPN: [...]
UPDATE: Friday, Sept. 13, at 2:45 p.m. ET
NFL Network's Albert Breer reports that Matthews has been fined for the hit:
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