Mourinho had publicly protested about the refereeing decisions involving Cuti Romero and Kang-in Lee after the match, even presenting a piece of paper showing the incidents at his press conference.
Atletico Madrid head coach Diego Simeone had already warned managers to be careful about their comments regarding referees.
“We are in a privileged position, with a very high profile as coaches and we have to be careful about what we say. We have to know how to respect the referee, our colleagues.”
Simeone added: “When you step outside that line of respect, no matter whether your name is Mourinho, Simeone, Flick or Pellegrini, you must not cross the line.”
Baena was even more direct when asked about Mourinho's reaction during an interview with Telemadrid.
“He complains because he has lost," he said.
"If it had happened the other way around, there would not be so much talk about this refereeing controversy and that's what always happens, that when Madrid lose against Atlético they try to look for other things rather than focusing on themselves.”
Baena also criticised Mourinho's decision to bring the incidents to his press conference.
“A tantrum? It can seem like that to me. The show with the pieces of paper seems like a tantrum and not knowing how to lose.”