The European champions had defender Gerard Pique sent off for a reckless challenge after 25 minutes at the Nou Camp and lost a second defender, Rafael Marquez, when he gave away a penalty in time added on.
With unbeaten Barca maintaining a five-point lead over Real Madrid, the Madrid-based sports media have claimed in recent weeks that the Catalans get favourable treatment from referees.
"It's really bad for football that every week doubts are being cast," Guardiola told reporters.
"Referees do their best and can make mistakes. It is such a great waste of time (to debate it) that it isn't worth it.
"It's as if Barcelona won six titles thanks to the referees."
The huge media coverage given to Cristiano Ronaldo's two-match suspension, after he broke Malaga defender Patrick Mtiliga's nose with a flailing arm, and Real Madrid's appeals to reduce the punishment has stoked the controversy.
"I have said plenty of times before the referees don't enter into my thinking," he added.
"I don't care if they leave us with 10, nine or eight players ... or if they blow for three penalties against us, we will have to score four.
"What happens (on the pitch) is our responsibility. The best thing to do is to look at yourself and with me that's what we'll always do."
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