Real Madrid go into Tuesday's tie at the Santiago Bernabéu on the back of a 1-0 loss at Betis, their first defeat of the season, with Troy Parrott's late goal deciding a match overshadowed by a stoppage-time penalty incident.
Kylian Mbappé's spot-kick, awarded after Vinícius Júnior was fouled, was saved by Álvaro Valles, but replays suggested Betis defender Marc Bartra may have encroached into the area before the kick was taken without VAR ordering a retake.
"We lost to Betis because we didn't convert our attacking play into goals. But regarding the penalty, why wasn't it retaken?" Mourinho said. "Is it because VAR didn't know the rules, or because they chose not to intervene? If they didn't know the rule, they should go home and not do VAR. If it was deliberate, that's even worse.
"I want to assume honesty and think they didn't know the rule, but I'd like people to answer me responsibly. The other thing, unrelated to the result, is why our captain Vinícius received a yellow card for approaching the referee to ask for an explanation, which he's entitled to do."
On his squad's mentality heading into the match, Mourinho insisted the dressing room had already moved on.
"I saw them exactly how I like to see them. They were devastated in the dressing room in Seville, and recovered by Sunday's training session. Today, completely normal," he said. "We're convinced we played well. The chances we missed were an anomaly. We have known problems, but that's it — we're going to play and compete."
Asked whether he draws more on painful Champions League memories at the Bernabéu or happier ones from his first spell, Mourinho declined to dwell on either.
"I've lost a semi-final on penalties here, but I don't think about that, positive or negative. I think of myself as the Real Madrid coach with a Champions League match tomorrow that isn't ultra-important," he said, adding that both sides would likely progress from the group regardless of the result.
The head coach also refused to confirm his midfield selection, with Bernardo Silva, Eduardo Camavinga and Arda Güler all unable to start together.
"I'm not going to tell you. The algorithm has decided," he said. On teenage forward Endrick, who trained with the first team for the first time on Monday, Mourinho was more forthcoming: "He could be ready for five or ten minutes tomorrow. He hasn't played since Budapest, so he's not in a condition for more, but we have space on the bench for him in an attacking role."
Asked about facing former player Cristian Chivu, now Inter Milan's head coach, Mourinho pushed back on suggestions of any rift.
"He was my player, we worked together, we went through good things and bad things together," he said. "Who have you spoken to, to know whether I have a bad relationship with him?"