The former Real Madrid and Chelsea manager saw his Roma side lose 2-0 to Inter Milan in a crucial game for the Champions League race.
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After Federico Dimarco's opener, Mourinho then let his frustrations get the better of him, chastising Nicolo Barella who had been fouled on the touchline in the 44th minute.
Leaving his technical area to be within feet of the Italy international, Mourinho gestured to him to 'get up' and Corriere dello Sport claim he said: "What the fuck are you doing?"
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Replays showed long-time Liverpool target Barella was taken down by Roger Ibanez, but Mourinho clearly didn't like the player rolling around in pain.
Tensions are clearly high at the Stadio Olimpico, with Roma going from third to seventh in Serie A within the space of a few weeks.
A defeat would leave them without a win in three games, and unlikely to qualify for European competition via the league table.
However, the Portuguese does have his side in the Europa League semi-finals where he takes on his former player Xabi Alonso who now manages Bayer Leverkusen. Victory in the competition comes with a place in the Champions League.
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Mourinho, though, appears to be feeling the heat, claiming he wore a wire during a 1-1 draw against Monza last time out for protection from the referee.
The incident is now being investigated by the Italian Football Federation after Mourinho said: "I'm not stupid, you know. Today, I went to the game with a microphone. I recorded everything. From the moment I left the locker room, to the moment I returned. I protected myself.
"He is the worst referee I have met in my life. He is the worst. Technically he's horrible. Zero empathy. Zero communication. Zero awareness.
"A second yellow to a guy who slipped in the 96th minute… I stopped talking 20-30 minutes from the end because I knew he would give me a red card for anything. I didn't give him the opportunity, I decided no, that's enough.
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"It's the limit of Roma as a club that doesn't have the strength of others to say 'We don't want this referee'. There are teams who say they don't want a referee, Roma don't have that strength."