Ross made his comment after the Pirates' 8-6 win over the Cubs on Thursday at Wrigley Field, their second straight victory over Chicago.
"That's not a good team that just took two out of three from us -- or not our caliber team, I believe," Ross told reporters.
Shelton laughed when a reporter wondered before Pittsburgh's game at Cincinnati on Friday if the Pirates manager had seen the comment.
"I saw them," he said. "It's unfortunate that he chose to make them about our team instead of his team. Over the last 60 games, we've played really well. I would rather focus on our club and the fact that we're playing good baseball right now.
"I know they won the season series against us, but I'm happy we finished strong against them. I'm more focused on the fact that we battled back against them after losing the first game to win the last two at their ballpark."
Pittsburgh went into Friday's game 72-81 overall and fourth in the National League Central. The Pirates were 11-8 in September and 31-29 over their last 60 games.
The Cubs are 80-74 overall and clinging to the third and final wild-card slot. Their 6-0 win over Colorado on Friday left them 3-7 in their last 10 games.