Gundogan stepped up to take the spot-kick after Raheem Sterling was fouled by Fabinho late in the first half, but put his effort over the bar.
The German midfielder, however, made amends by scoring twice in the second half, as City recorded an emphatic 4-1 win at Anfield.
“Gundogan missed a penalty, it’s like a routine against them, but we started really really well, doing what we want to do,” Guardiola told BBC Sport.
Turning his attention to the penalty miss, Guardiola added: “It’s a problem that we have. In important moments, we cannot miss it, and it doesn’t matter the taker.
“Again, I’m going to think about Ederson, he might be the taker next time.”