Mijatovic says Real lost the game due to coach Zidane's team selection.
"It started when preparing for this match, knowing that Alaves have three players up top who are their strongest players," Mijatovic said on Cadena Ser's Carrusel Deportivo programme.
"Lucas Vazquez played a good game against Inter when he played further forward as a right winger, so you can't move him back to right-back for this game.
"You've got Eder Militao who can play there, but I don't know what's going on with this kid. He's not playing as a centre-back or as a full-back.
"I feel like they didn't realise that Alaves' strongest areas are the left wing and up front, with their two strikers. That's where the problem started.