Barca felt they should have had a spot-kick in the goalless draw when Christian Abbiati brought down Alexis Sanchez right in front of the additional referee's assistant placed behind the goal in Champions League matches.
However, neither the assistant nor referee Jonas Eriksson spotted the foul.
Guardiola said: "What's the use of two extra goal-line referees if they don't see clear penalties? If they don't give it, they didn't see it."
Barcelona captain Carlos Puyol also felt he should have had a penalty for shirt-pulling in the second half.
He said: "Penalty? Yes, I was clearly held back, you could it see on the screen too, but the referee said no. His task isn't easy, no excuses."
Guardiola said he was satisfied with his team's performance, if not the result, but was unhappy with the state of the San Siro pitch, which disrupted Barca's slick passing play.
He said: Maybe we deserved a goal, but we'll have to win it at the Camp Nou. We hope for the fans' support.
"That Milan, a team with seven European Cups, is happy about this 0-0 result, is the best praise we can get.
"(The pitch) was slippery. At half-time, we told the players to be careful not to get injured.
"It's a great stadium, but it's quite closed and the pitch can't breathe. It's always bad, but it is what it is.
"To win the Champions League, you have to overcome a lot of things, that's what makes some sportsmen better than others," Guardiola added.
"Things happen and you have to overcome then."
"We have won a lot in the last four years, but we have also drawn and lost matches.
"After a draw or defeat, we have never complained about a refereeing decision or the pitch, maybe we have done so after winning but not after a draw or defeat."