Matt Grimes opened the scoring for the Championship side after converting from the spot kick.
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The visitors upped the ante after the break and pulled one back through Bernardo Silva, before an Aguero penalty went in off goalkeeper Kristoffer Nordfeldt.
"If it is not penalty, and it is offside like the people say, I'm sorry", Guardiola said.
Raul Jimenez and Diogo Jota sent Wolves into the semi-finals of the FA Cup for the first time in 21 years with two goals in six second-half minutes, with United only having Marcus Rashford's late consolation to show for their efforts.
VAR cameras are installed at all Premier League grounds, so the facilities are used by the FA during their Cup games.
Speaking in his post-match news conference, Guardiola said: "All around Europe there is VAR, here there is not".
Sergio Aguero was then in an offside position when he scored the victor in the 88th minute, but the Video Assistant Referee was not in use as the game was not being played at a Premier League ground. "But the spirit and persistence helped us to win the game".
Those are the two stadiums where Premier League clubs are playing in the quarter-finals of the competition.
"We try to play that way", Swansea manager Graham Potter said of the second goal.
"But it does not make it any easier when Aguero and Sterling come on, it makes it more hard and in the end we couldn't hold out".
For a long time, the story of the game looked like it would be all about Celina, a player who joined Swansea from Manchester City and someone Guardiola knows all about.
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