The Spaniard made eight changes to his side after beating Borussia Dortmund during the midweek in the Champions League, and Thomas Tuchel, whose Chelsea side had an extra day of rest, made just three changes.
Ruben Dias, Rodri, and Kevin de Bruyne were the only players to keep their places from Wednesday, while Hakim Ziyech, who scored the winning goal in Saturday's semi-final was one of changes made by the Blues boss.
"What could I say? We had two-and-a-half days to recover and play away and have to travel, we were on the train for three hours and we were stopped one hour," Guardiola said.
"Everyone deserved to play, don't say we don't pay attention, when this team reached four finals in a row in a Carabao Cup. Just say we lost the game and when we lose the game the decisions are bad but it is a poor argument. You don't get to the semi-finals of the FA Cup or final of the Carabao Cup four years in a row when we don't pay attention.
"Say it before the game that Pep doesn't pay attention or the players don't, but don't say after just because we lose the game. These guys fight every game like never before I've seen. Now we don't pay attention?
"We respect the FA Cup a lot, we come here to win and next time tell me which people say that. Do you think [Raheem] Sterling, or Gabriel [Jesus], or Ferran [Torres] don't deserve to play the game? Say it."
Meanwhile, De Bruyne's injury added additional concern for Guardiola ahead of a crucial run of fixtures, which includes the weekend's Carabao Cup final against Tottenham, and their Champions League semi-final against Paris Saint-Germain.