The Real coach waved a piece of paper listing 13 supposed errors by Carlos Clos Gomez at Sunday's post-match press conference.
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"Mourinho's stance is that of a crybaby," Emery told reporters. "We have reasons to draw up a list with errors and to make a public complaint for every time we have been adversely affected, but we don't."
Mourinho complained that the club needed to back him more by speaking out against perceived refereeing injustices.
"My team needs to be defended," he said. "If I say what I think I will be on the front pages and suspended. There is a club and a structure and I want them to defend my team from there."
VIDEO:See Jose's post-game whinge in Monday's La Liga Loca
Athletic Bilbao boss Joaquin Caparros labelled Mourinho's complaints a strategy.
"I don't take any notice of it," he told reporters. "It's all part of the world of football. I am sure that Sevilla will be preparing 20 points on the refereeing."
After the match, Sevilla president Jose Maria del Nido said: "The pressure they (Real) put on the referee can be seen by the whole of Spain. It is a pre-meditated, coached and designed tactic but we already know what it is to play at the Bernabeu."
The victory kept Real two points behind leaders Barcelona after 16 matches following the champions' 5-1 destruction of city rivals Espanyol 5-1 on Saturday.
NEWS:Ten-man Real Madrid scrape past Sevilla
