Aubameyang was previously suspended by the club last November when he missed the 1-0 win over Sporting Lisbon in the Champions League for a trip to Milan against then-coach Thomas Tuchel's wishes.
"But I don't understand it this time - I didn't want to turn up late".
German newspaper Bild reported how Aubameyang used two days off granted by the club during the global break to visit former Dortmund team-mate Ousmane Dembele.
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"After my trip to Milan I could understand my suspension because I ignored an announcement that time".
However, Bild reports the striker has been repeatedly late for training, with the latest offence coming when he arrived 20 minutes late for final preparations ahead of the trip to Stuttgart. But the club are not in such fine form at the moment.
After Stuttgart, Dortmund meets Tottenham Hotspur in the Champions League and regional rival FC Schalke in a vital derby.
The Gabonese forward is the club's top marksman with ten Bundesliga goals so far, but he has failed to score in the past three games with Dortmund in a slump.