The Red Devils were handed a red card following a reckless challenge by Victor Lindelof on 83 minutes, but the Video Assistant Referee overturned decision and the defender was only handed a yellow card.
They are top of the Premier League, in the Champions League quarter-finals and have already won the League Cup.More news: New Zealand mosque attacks death toll hits 50
But while VAR will be used at some FA Cup games, it was not in use in Wales and the decisions were upheld unchecked.
In reality, the Citizens more than deserved the win.
Ironically Swansea had access to the system in the quarter-finals a year ago - while still in the Premier League.
"People will say not winning the Champions League is a big, big failure for this club but I don't understand when this comes from former players - they know how hard it is to win the Champions League or win the title", Guardiola said.More news: Australia now eye World Cup crown
City, who last won the FA Cup in 2011, showed their fighting qualities as they survived a scare against Swansea thanks to Sergio Aguero's late victor.
Sergio Aguero popped up with a winning header just minutes from full time to sink Swansea hearts.
"If it is not penalty, and it is offside like the people say, I'm sorry", Guardiola said.
Pep Guardiola's team roared back from a two-goal half-time deficit to score three times after the break, with Sergio Aguero grabbing a disputed late victor in a 3-2 victory. "Hopefully, next season this won't happen".More news: Dem lawmakers grill Ross on citizenship question - Newswatch
The technology is in use in the FA Cup and was available at the Liberty Stadium last season, but the Football Association is reported to have opted against equipping the ground with VAR since their relegation to the Championship.