The Premier League side struggled to break Swansea down after the break, but Bernardo Silva's goal in the 68th minute got the visitors back in the match.
City's Fabian Delph was sent off in that game at the DW Stadium and against Swansea the same player was shown a yellow card which led to a penalty, slotted home by Matt Grimes after 20 minutes.
Then Bernardo Silva pulled one back, a most generous penalty gifted them an equaliser, and Sergio Aguero scored an offside late victor.
"If it is not penalty, and it is offside like the people say, I'm sorry", Guardiola said.
Aguero missed a glorious chance to score but the Argentine striker had the final say when he headed the victor two minutes from time from what looked an offside position. "I don't like to lose games when the decisions are wrong but the referees don't want to make wrong decisions, but they must be helped".
The Premier League leaders mounted a stunning recovery to overcome the daunting deficit after Sterling and Aguero entered the fray either side of the hour mark but the win was achieved in controversial circumstances with the equaliser and Aguero's victor hotly disputed. I don't understand why VAR is not used in this competition at this stage.
Swansea then carved City open with a slick passing move and it was superbly finished off by Celina. "We had composure, shape, good running", said Wolves manager Nuno Espirito Santo.
Guardiola said: "You have to say congratulations to Swansea, it was incredible". Aguero's spot-kick bounced back off the post, only to rebound off keeper Kris Nordfeldt and into the net to bring them level.
"They ask all the clubs about the VAR (video assistant referee) and all around Europe the VAR is there and here it's not". "Here there is not".
"I don't like to win it this way, but at the same time if you see the game we played incredibly well".