Cardiff had been heading for a win until Chelsea captain Cesar Azpilicueta headed in a late goal despite appearing to be offside. Chelsea then scored one more to take all three points.
"Is there someone who cannot understand his reaction (to Sunday's decisions)? It is tough for managers, clubs, and players who want to stay in the Premier League," Guardiola told reporters on Tuesday.
"It's a big issue. We have empathy with his position, we can understand completely."
City, who are two points behind league leaders Liverpool, will return to the top of the standings if they beat 18th-placed Cardiff on Wednesday.
However, Guardiola said his side would still be motivated to play against a team that has lost four of its last five games and nearly beat Chelsea.
"Cardiff are alive, based on what I saw against Chelsea," Guardiola added. "It's not a team that is already done. We know how we are going to play and it is a final every game. It (motivation) will not be a problem."
City striker Sergio Aguero, who leads the league's goal scoring charts with 19 goals, will not be available after picking up a hamstring injury in the 2-0 win at Fulham over the weekend, with Gabriel Jesus expected to start instead.
"He (Aguero) didn't train for the last two days, and tomorrow he is not able, so hopefully (he will be ready) for Saturday or Tuesday," Guardiola said. "We will see the evolution in the next days."
(Reporting by Rohith Nair in Bengaluru; Editing by Hugh Lawson)
