Dejan Kulusevski's early opener was cancelled out by Gundogan's composed finish, before Harry Kane restored the visitors' lead in the second half.
Riyad Mahrez equalised from the penalty spot in stoppage time, but Kane found the net again minutes later to snatch the three points.
"If you look at the whole game we deserved to win, but football is sometimes crazy and today we made easy mistakes.
"We gave them the ball to have possibilities to counter and that made us lose the game.
"They were also ruthless in their finishing up front. We had a lot of chances and the possibility to score a few more goals, but we gave them the chances they had too easily.
"It didn’t feel like a bad game from us. They defended so, so deep, particularly towards the end of the first half. It’s not so easy.
"Sometimes you have these kind of games and you need to learn from it. It’s a wake-up call for us. There’s still a long way to go."
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The loss keeps City at the top of the league, six points clear of Liverpool, who have a game in hand.
The 31-year-old is expecting a big push from Jurgen Klopp's side but feels there's no reason to panic as there is still a long way to go until the end of the campaign.
“It’s not a situation that we’re not used to. We know from recent years that Liverpool are always contenders. They’re always up there. We know they’ll try everything to make our lives as difficult as possible.
"The good thing is that they still need to come here to the Etihad, but there are still many games to go.”