Arsene Wenger said he was "revolted" by the referee after his "brave" Arsenal side suffered a last-16 Champions League thrashing by Bayern Munich.
Referee Anastasios Sidiropoulos denied the hosts a penalty when 1-0 up before later awarding one for a Laurent Koscielny foul on Robert Lewandowski.
Koscielny was sent off as Arsenal lost 5-1 on Tuesday and 10-2 on aggregate.
"The penalty and red card are absolutely unexplainable and scandalous," Gunners boss Wenger said.
"It's irresponsible from the referee. It leaves me very angry and very frustrated."
Arsenal faced an uphill struggle going into Tuesday's second leg having suffered a 5-1 defeat in Germany three weeks ago.