City have collected six red cards this season including two on Saturday when Aguero and Fernandinho were sent off.
City have collected six red cards this season, including two on Saturday when Aguero and Fernandinho were sent off towards the end of a 3-1 Premier League defeat against Chelsea.
Aguero has received a four-match ban after being dismissed for a wild late challenge on David Luiz, having already served a three-game suspension this season for elbowing West Ham's Winston Reid.
To make matters worse for City, Fernandinho has been banned for three games following his red card for pushing Cesc Fabregas over an advertising hoarding during the angry confrontations that followed Aguero's tackle.
Guardiola believes it is unusual for a team who have enjoyed so much possession during matches to collect so many red cards, in what could be perceived as a criticism of referees.
"The referees, I don't talk about. It is better that way. We are the best team with ball possession and with most red cards," Guardiola said on Monday.
"It is a pity what happened in the last minute and of course we are going to accept the ban from the FA. We are going to work with other players for the next games."
After brushing aside the disciplinary problems, Guardiola insisted his team are progressing in the right direction despite a shaky run of form that has seen them fail to win a Premier League home game since September 17.
"Of course I would have preferred to have won against Chelsea and we would be top of the league. Then our analysis would be completely different," Guardiola said.
"But I'm confident because we played 60, 65 minutes of good football. We need to continue, continue, continue and when we do, we'll be there."
Aguero is in contention to play for Manchester City against Celtic in the Champions League on Tuesday, even though Guardiola planned to rest him before his sending off.
The Argentina striker will not be able to play for City in the league again until December 31.
Guardiola is planning changes to keep his squad fresh for a series of vital games in the run-up to Christmas, but there is now no need to keep Aguero in reserve.
"There will be changes tomorrow, definitely. I am so happy to give minutes to people who deserve to play and who did not play in the last games," Guardiola said.
City are guaranteed to finish second in their Champions League group whatever happens on Tuesday, while Celtic are certain to end up bottom.
"I would prefer to finish first," Guardiola said. "I don't know why but I prefer to. It's more for the club because you won more games.
"But from my experience in the Champions League, it is how you are playing in February."