In reality, the Citizens more than deserved the win.
City had levelled in contentious circumstances too when Cameron Carter-Vickers was judged to have tripped replacement Raheem Sterling in the area and Aguero's penalty hit the post before rebounding in off Nordfeldt for an own goal.
The Liberty Stadium is equipped for VAR but because other Championship grounds are not, it was not operated for the sake of consistency.
"If it is not penalty, and it is offside like the people say, I'm sorry", Guardiola said.
"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.
Aguero then completed the turnaround at the end with a header despite appearing to stray offside and, had VAR been in use, their second and third goals arguably would have been disallowed.
"They ask all the clubs about the VAR (video assistant referee) and all around Europe the VAR is there and here it's not".
"That seems a bit odd considering we were there for seven years and all the technology is placed here to accommodate it".
Guardiola said: "You have to say congratulations to Swansea, it was incredible".
"But we didn't give up".
"I want to congratulate the team and everybody. The performance was one to be very proud of". "It's not nice but thankfully nothing happened this time".