Liverpool lost 1-0 at Anfield after Kai Havertz scored the only goal in the 16th minute, but the result was overshadowed by a controversial first-half incident involving Isak and Arsenal defender Jurrien Timber.
Isak was attempting to reach a cross when Timber pulled his shirt inside the penalty area. The Liverpool striker remained on his feet and failed to make contact with the ball, while referee Andy Madley waved away the appeals.
VAR reviewed the incident but did not recommend an on-field review, leaving Liverpool furious that a penalty had not been awarded.
Iraola was particularly frustrated by the suggestion that Isak should have made more of the contact to convince the officials.
"The Isak one is a clear penalty, they grab him, everyone see the shirt and probably because he doesn't dive," the Liverpool manager said.
He went further when asked whether the striker should have gone to ground.
"The fact that you are even asking me this question but honestly, yes, if you don't go down," Iraola said.
"I think Alex is honest, everyone can see straight away it is a clear pull. I can say what I think about the situation but we have to say what it is, it is a pen."
The Liverpool manager then made clear that he would change his instructions to players in similar situations.
"If he goes to the floor, they call the penalty for me. They call the penalty, 100 per cent."
Iraola also pointed to the possibility of receiving an explanation from the Professional Game Match Officials Limited, although he accepted that any subsequent clarification would not alter the result.
"I think we have to wait now 10 days or 12 until (Pro Ref) give the solution but it is not going to change anything. It was a clear penalty for us."
The incident came during a difficult afternoon for Liverpool, who had chances to equalise but could not find a way past Arsenal's defence. Wirtz hit the crossbar with a free-kick and Mac Allister headed over, while Isak also failed to convert a later opportunity.
The defeat gave Arsenal their first league victory at Anfield in 14 years and sent them three points clear at the top of the table. For Iraola, however, the penalty decision was likely to remain a major talking point after a match in which he felt his side had been denied a clear opportunity to get back into the contest.