City have been referred to UEFA's adjudicatory chamber for alleged breaches of financial fair-play rules (FFP), where if found guilty they could face expulsion from the Champions League.
It has slightly overshadowed City clinching their second successive Premier League title last Sunday, while victory at Wembley on Saturday would secure a historic domestic treble, but Guardiola is critical of how his club have been condemned by many already.
"I trust the club and the people," he said. "I know we won the Premier League and in the last two or three days, people only talked about this (the alleged breaches).
"If we did something wrong and UEFA decides that we did something wrong, we will be punished or whatever they decide.
"I know people are waiting for us to be guilty. But we are innocent right now.
"Sometimes it's difficult to understand for everybody because it doesn't always happen all over the world, but we are innocent until proven otherwise."
Guardiola said he would leave the arguments to the club's lawyers.
"We will accept it but I have spoken to the Chairman and the CEOs. I know exactly what they did and I trust the lot of them," said the 48-year-old Spaniard.
"UEFA are now working with the lawyers of Manchester City. Manchester City is open to expose all the papers, all the documents and all that they have done.
"I am not a lawyer. I don't know what is going to happen behind the scenes in all the meetings they have.
"Today we are innocent. We will see in the future."
As Guardiola prepares for the clash against Watford, he also had to defend his players and backroom staff.
Footage emerged from City's private plane back from Brighton last Sunday of a chant being sung, which has offended those connected to Liverpool due to lyrics talking about them as "victims" and "getting battered in the streets".
Some people said the lyrics refer to the Hillsborough tragedy and the stabbing of Liverpool fan Sean Cox before last year's Champions League semi-final against Roma.
However, Guardiola has apologised and insisted there was no intention to mock their Premier League rivals who kept the title race alive until the final day of the season to finish one point adrift of City.
"We were happy for ourselves, not because we are for the other ones, so if someone was offended for another issue, I am sorry," he said.
"I apologise but it was never our intention.
"We celebrated for ourselves. We were happy to win the Premier League. It was so difficult against an incredible contender.&quoRead More