Guendouzi had a "lively altercation" with Tudor during their 2-0 defeat to AC Milan last Sunday as their pre-season has been filled with unrest behind closed doors.
Jordan Amavi and Gerson have also had issues with the new boss, says L'Equipe.
The French publication reported that Guendouzi had an 'altercation' with the manager as Marseille trailed 2-0 at half-time during last Sunday's friendly defeat to Milan. The Frenchman then went off to shower, packed up his things and was nowhere to be seen for the second half.
The squad were extremely fond of former boss Jorge Sampaoli, who left over a disagreement over transfer policy.