The 28-year-old has been dropped from the squad to face Stuttgart on Friday evening due to disciplinary reasons, thought to relate to a trip to Barcelona during the international break.
Separate reports in the German press suggest that Aubameyang has been suspended due to a lack of time keeping in training, but the Gabon international - linked with summer moves to Chelsea, Manchester City and Paris Saint-Germain - claims that he has done nothing wrong.
Aubameyang, also penalised by Dortmund last year for an unsanctioned trip to Italy, told Bild: "I didn't turn up late for training. After my trip to Milan I could understand my suspension because I ignored an announcement that time. This time I really can't understand it."