While battling for the outer reaches of the points late on in Saturday's crash-strewn sprint race at Jerez, Marquez collided with Honda's Mir at the last corner as he made a failed overtake attempt.
Mir took a strong hit and lost several places, ultimately finishing out of the points in 10th.
Gresini rider Marquez, who crashed out of the lead on lap nine, was ordered to drop one position by the stewards for the clash but still scored points in seventh.
Mir felt the punishment Marquez got was "unfair" as he feels he was given a harsher penalty for a collision with Fabio Quartararo in the Portugal sprint last year, and took aim at what he feels is the stewards' lack of consistency.
"It was a bit unfair because I think I made a really good start, then I had the contact in Turn 2," Mir reflected.
"Then I lost a lot of positions and then I started to break away from the group I had behind to the guys in front. I overtook the group with Miguel [Oliveira] and then I stayed behind Raul [Fernandez] to prepare one attack for the last laps.
"Then Marc just came at the last corner, he touched me, he hit me out of the track, I lost all the positions.
"Then when he overtook Miguel in the same exact way, [and] he was demoted [only] one position and that's it.
"So, the last time I received a penalty was in Portimao in the [2023] sprint race, similar thing. I braked, I overtook Fabio, I lost the front, I kicked Fabio out and he lost a couple of positions.
"I crashed and for the race on Sunday they gave me a double long lap.
"That was the last penalty I got. So, this time he didn't crash, he hit me out of the track, I lost four positions – [he is] demoted one position. I want to understand.
"This is something that when I went into the box I was with a poker face because I say 'how is this possible that one rider you say one thing, and for the same move or even worse it's [only] demoted one position'."
Mir added: "I'm not pissed with the manoeuvre from Marc, because if he waited three seconds more we pass the corner and in the straight he overtakes me.
"So, this is something that I don't really understand being in that position.
"If we fight for the podium I understand. But man, it's unbelievable how they value these types of things, and they are so irregular with penalties. It's unbelievable.
"In the end, I'm a rider who in the past liked to overtake with contact. It's something that I do because nowadays with the aero it's very difficult to overtake.
"So, with a bit of contact, we have to have this margin in the overtakes. But one thing is the margin to touch and open your line, and the other thing is to kick the rider out of the track.
"This is a completely different story. They have to judge as they did in the past."
Asked if he felt Marquez's overtaking was over the limit, Mir replied: "He came into my line, he kicked me out of the track to get that position.
"This is something at the moment you cannot do. Or if you do, you have to be penalised."
Marquez felt his penalty was "good for the stewards" and feels Mir "tried to insist" on the brakes in his defence.
"Was exactly the same situation as with [Brad] Binder,” the Gresini rider remarked. "Binder overtook me and then I saw him and then I saw and pick up the bike.
"I try to overtake Mir in a smooth way, but then he released the brakes and go in and then we had the contact. Was my fault but yeah, sometimes you need to understand.
"For example, with Binder I was able to go in and had the contact, but then I know that I will lose not only with Binder, I will also lose more positions.
"So sometimes you need to analyse. But in that case Mir tried to insist and I didn't release the brakes enough to overtake him completely.
"I take the penalty, one position, was a good penalty for the stewards but it was easy to drop a position to Oliveira and come back from there as well.”
