The Spaniard saw his team's winless run stretched to three games after the 1-1 draw against the Toffees as, despite enjoying 72 per cent of possession, City missed two penalties.
Romelu Lukaku scored for Everton, albeit against the run of play, with City needing Nolito to come off the bench and rescue a point.
Guardiola, who saw his 100 per cent home record in charge of City ended, warned that there would be more matches like that to come in the future.
"We did everything and I am so proud of that team. We played amazing. We created chances, had two penalties. They had one chance. In football it is like this. Big compliment to Everton about the way they defend and their performance," he told BBC Sport.
"I am sad for the players because they deserve to win the game. We have to keep our heads up because from the beginning of the season we have done so well. Football is football. This happens sometimes. We did absolutely everything. Everton create just one chance which was a goal.
"I'm a little bit sad and disappointed for the players. But it's a big compliment to Everton and Ronald Koeman so I say to them 'well done'. The players have all the qualities to score penalties but we miss a lot. Hopefully we will score more of them in future. It won't be the first time or the last time we have a game like this."