But Bayern's defending concerned Kovac ahead of the first leg of their Champions League last-16 tie against Liverpool at Anfield on Tuesday, with his side having now failed to keep a clean sheet in six games in 2019.
"This [defensive mistakes] cannot happen to us at Liverpool," the Croatian told a news conference.
"When my players at Liverpool start letting people go, especially with the front three there [Mohamed Salah, Sadio Mane and Roberto Firmino], then we will find ourselves in a very dangerous situation every minute.
"That's why it's important to have the ball to take responsibility and act in a disciplined way.
"Then you can defend something, but if you let the opponents run, then every team in the Bundesliga has the quality to score."
Kingsley Coman scored a brace for Bayern and set up David Alaba's winner, before coming off with an ankle injury.
The 22-year-old twice drew his team level after a Leon Goretzka own goal and Ji Dong-won strike for Augsburg.
Kovac, who is hopeful over Coman's availability for the trip to Anfield, said Bayern were still not where he wanted them to be when out of possession.
"I think it felt like three shots from Augsburg and two of them scored. That's what basically haunts us throughout the season – every shot is a goal," he said.
"And if we don't have the ball, we don't act as I imagine. We know that our individual mistakes mostly result in goals."