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The Spaniard made the claim on a Twitter Q+A, and believes his teammates do not see the runs which Werner makes in a game and often fail to pick him out.
The fan asked the 2010 World Cup winner for his opinion on the German, to which he replied: "He makes so many good runs but sometimes they either don't see him or don't play the pass. He looks fed up sometimes."
He makes so many good runs but sometimes they either don't see him or don't play the pass. Looks fed up sometimes :joy: https://t.co/USfJNDkkNb- Cesc Fàbregas Soler (@cesc4official) October 28, 2021
Werner arrived at Stamford Bridge for a £47million fee after scoring 95 goals in 159 appearances across all competitions for RB Leipzig, but has failed to transfer that form in a Chelsea shirt.
The 25-year-old was clearly delighted to get off the mark after having his fair share of goals called off for marginal VAR calls.
"I was very happy to score and help the team,' Werner told Chelsea TV in quotes published by the Mail Online. "In the first half, it was the story of my whole Chelsea career in one game a little bit!
"It was obviously not so clear because it took the referee a while to make his decision. Maybe 50/50. We have to accept it, I had to accept it, and in the end, I was happy I could score again and we won the game.
"It was a very important win after losing the last two. It was a very tough game for us because Southampton did very well."
Timo's goal struggles were clearly playing on Thomas Tuchel's mind too, who has kept the faith in his compatriot.
"We are all relieved, him and me and the whole club,' Tuchel added after the game.
"Every time he scores we have the feeling there is a VAR decision to take it away from him, there have been a lot of very narrow decisions. I remember one against Liverpool that was super close.
"He has to keep on going and a lot of things to improve. We're happy and relieved that he scored. It was very, very important goal for us to secure the win. And on the other hand, he was there when he needed to be."
Tuchel's men are back in Premier League action on Saturday when on Newcastle United at St James' Park.