Brahim Diaz and Jude Bellingham struck late to erase City's 2-1 lead, the latter netting the winner in the 92nd minute at the Etihad Stadium.
"We arrived at the last minute with a result and we could not keep it," Guardiola told a press conference.
"After 2-1, many games it has happened, against Feyenoord in the UCL (City led 3-0 in the 74th minute but ended with 3-3 draw), against Brentford in the Premier League, against Manchester United, many games at the end we give away," he added.
"Unfortunately it has happened so many times."
Erling Haaland's double, including a penalty in the 80th minute, had City poised for a win over the holders and LaLiga pacesetters but leads have proved slippery this season for Guardiola's side, who are fifth in the Premier League.
They have conceded seven goals in the final 15 minutes of Champions League matches this term.