The 25-year-old was booed off the pitch with his side trailing and desperately searching for goals to progress to the next round.
The episode is the latest set-back the former Lyon midfielder has suffered in North London, and with his future now hanging in the balance, here are five reasons why Tottenham fans seem to have had enough of the midfielder.
Asking to leave the club in the summer
Last summer was a very difficult period for the French midfielder, especially as he saw his two most reliable friends, Moussa Sissoko and Serge Aurier, leave the club.
His own future was up in the air with reports that he’d asked to leave the club under then manager Nuno Espirito Santo.
The fans knew what was going on, but were counting on his brilliance and hoping that he could come good this season.
But the season has been one to forget, and it all came head on against Morecambe.
Falling out with Jose Mourinho
Jose Mourinho publicly criticised the midfielder and questioned his application, after a below par performance against Burnley in the Premier League.
The now AS Roma boss said back then: “I know the Premier League is difficult, and some players take a long time to adapt to a different league.
“But a player with his potential has to give us more than he is giving us, especially when you see how Lucas [Moura], [Giovani] Lo Celso and those players are playing.”
At that time there were fans who thought Jose Mourinho was being too hard on him, but having failed to step up for Nuno and now Antonio Conte, the fans are getting frustrated with his perceived lack of effort.
The midfielder’s body language on the field
Andrea Pirlo, Juan Román Riquelme and to a lesser extent Santi Cazorla all played the game at their own pace, and dictated the speed at which they wanted a football match to be played.
You sometimes get the feeling from watching Ndombele that he is that kind of a midfielder, except that he doesn’t influence games like those players did.
Those midfielders barely broke sweat but everything good in their respective teams started with them.
If you’re not going to be covering every blade then you must be setting up goals and making game-changing moves.
The French midfielder hasn’t been great in deciding games and fans are now picking on his style and thinking he is not doing enough.
Falling out with Nuno Espirito Santo
One of the first challenges Nuno Espirito Santo encountered at Tottenham was trying to convince Tanguy Ndombele to get his mind and body in shape.
The former Spurs boss, like his two predecessors Pochettino and Jose Mourinho, had seen enough in training to know he is a special talent, but could see the French midfielder was missing something.
Nuno Espirito Santo said back in August 2021: “What I can tell you is that Tanguy is with us, he works, but we have to speak honestly and to take the best out of Tanguy - (it) has to come from himself.
“We already had a chance to talk but it must have come from him.
“I said it before, my job here is not to convince players to play for Tottenham Hotspur, it is to prepare players to play for Tottenham Hotspur.”
He did manage to get himself back into Nuno’s team but the performances never really matched the expectation from both fans and manager, before the Portuguese boss was shown the exit door at Tottenham.
Antonio Conte questioning his ability to be a team player
One of the first players Antonio Conte questioned when he took over Tottenham was the French midfielder.
The Italian manager, just like those before him, had found a genuinely gifted footballer, but was frustrated by something and wanted to fix it.
Conte told the press he was working with the midfielder, but was urging him to be less about himself and more about the team.
He said: "I have seen that many managers struggle with this situation, about his position.
“For sure Tanguy has the quality. At the same time, he has to understand that there is a team and he has to play into the team.
“I think it means that it is important to keep order and to do what the position asks you to do.”
Since Conte made these comment, Harry Winks and the ever-impressive Oliver Skipp have had more game time than the £5million record signing from France.
It will be interesting to see what he does next with reports that Antonio Conte might be planning to say goodbye to him this winter transfer window.