Jones appeared in a radio interview for 105.3 The Fan in Dallas and talked about Kaepernick's workout. He said last week that he wasn't attending, nor would there be a team representative at the event.
"That situation from the get-go probably had a lot more that wasn't about football involved in it and consequently we got the results of that dynamic," Jones said.
Asked outright whether he thought Kaepernick's incident was turned into a "circus," Jones replied, "I think so."
"We, of course, aren't in the quarterback business," he said. "We're in the business of anytime, anywhere looking for talent -- whether we need it now or whether we need it in the future."
He added: "So, the way these things work, you had that evaluation for you whether you're there or you're not. You have that evaluation. And, I think it's unfortunate that you can't just zero in on the business at hand, and that is evaluating a player that might or might not help you win a football game or move the chains within a football game."
Jones also made clear that he believed the team was set for the future with Dak Prescott as the starter and Cooper Rush as his backup.
Kaepernick moved workout locations from the Atlanta Falcons training facility to a high school 60 miles away. His representatives made clear they wanted the workout to be more transparent with the media and took issue with the waiver the league wanted him to sign.
Only eight teams showed up for the workout session after Kaepernick announced the move.