The Red Bull driver failed to make it into Q3 at the Red Bull Ring after failing to set a clean lap during the session.
And while being clearly outside the white lines in the first two runs, Perez thinks it's unfair that he was also penalised on his final effort when he felt he had been disturbed by the Williams of Alex Albon.
"There's so many things I can control and unfortunately, with this one, you're closing a good lap and then all of a sudden you are blocked, and you have a penalty," he said.
"I think the system is wrong. It is just frustrating that we don't have a good system and we are not able to consider when these things happen."
Perez was aware that everything hung on the final run but reckoned it was all under control until traffic got in his way.
"I was on a good lap," he said. "But then all of a sudden on my final lap, I found I think Albon, and I just went straight. I could not stop. I think I lost a 10th or a bit more than that just by going straight, but the stewards wouldn't consider that I was blocked."
But despite Perez blaming traffic for his Q2 exit, his Red Bull team boss Christian Horner felt that the Mexican should have done a better job in taking fewer risks when he knew that he had one final go to get a lap in.
"It was crystal clear," Horner told Sky. "The frustrating thing is we know he can do it. He did a 1m04.9s on that lap, and he was three hundredths off Max. He could have been four tenths slower and still been in.
"So I think Q2, that's not the time to be doing it. That was the frustrating thing, because he could have done it today."
Asked if he felt traffic had hampered Perez, Horner said: "There's a car ahead and, of course, it is not going to have helped. But then you build in a little bit more margin. Checo is frustrated but will turn the page. He'll race hard tomorrow.
"But it's just annoying, because we know he could have been there."
