The bizarre situation recently came to light after the Ligue 1 giants suddenly put the Frenchman on the market in a move that shocked the club's supporters.
Clauss, a £7.9million signing from Lens in 2022, has performed admirably since his arrival at the Orange Velodrome.
This season alone, the 31-year-old has featured in 19 of Marseille's 20 league games and all six of the club's Europa League ties.
As an important member of head coach Gennaro Gattuso's squad Clauss appeared indispensable… or so it seemed.
Clauss was put on the market by Marseille president Pablo Longoria in the final hours of the January transfer window in a bid to force him out of the club.
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However, the France international refused to leave and his failure to secure a move away has seen the club dispute the claims.
According to French sports outlet L'Equipe, the breakdown between the two parties began when Clauss pulled up with an injury in the 2-2 draw against Monaco on January 27.
After medical staff examined Clauss and told him that tests showed his issue was nothing serious, club chiefs became furious that the players did not finish the match and accused him of not giving 100 percent effort for the club, instead focusing on being fit for this summer's Euros.
Marseille believed it was the third time Clauss has not committed his body to Marseille after similar incidents in October and December.
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L'Equipe claimed the club's opinion on Clauss was leaked to the press to help speed up January exit.
The outlet also reported that on the night of the Monaco clash, sporting director Mehdi Benatia sent a voice note to Clauss's entourage explaining how he would never wear a Marseille shirt again.
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The next day, Longoria, and Gattuso met and agreed to find a way to oust Clauss from the club.
The player was subsequently asked to stay away from the club due to being too much of a disruption to the team since his call up to Didier Deschamps France squad in 2022.
This reportedly included being too loud in the dining room and being critical of teammates when they made a mistake with the ball.
Marseille were forced to cool tensions when it became clear that Clauss was not going to leave in January with general manager Stephane Tessier telling the player that the situation had been blown up by the media.
Clauss made his comeback in last weekend's 1-0 defeat at Lyon, coming on as a second-half substitute but the unknown awaits when he takes to the pitch for Friday's clash with Metz - his first at the Velodrome since the affair.
Gattuso told reporters ahead of the game: "Clauss is an important player but you have to ask more, like with others. This is what we are missing, being demanding with ourselves and with others, reproaching your partner if he does not do enough, everyone must make themselves available to the other without thinking individually."
Meanwhile Longoria added: "Clauss must be an important figure and this involves all the little daily attitudes. This week he had a very good reaction."