The Gabon international was dropped from the squad by then-boss Peter Bosz in November ahead of the Bundesliga meeting with Stuttgart, which was reportedly down to an unauthorised break.
Aubameyang, linked with a move to Chelsea during the summer transfer window after topping the German scoring charts last term, has now been warned by Zorc to abide by club rules.
"Auba is a special player. He is extravagant and a colourful character," he told Sky Deutschland. "That does a city like Dortmund a lot of good.
"We have only one problem with him - that is punctuality. We have to be very clear about that. This crept in last year, that he often arrived too late.
"His pal [Ousmane] Dembele was right there. Then, as a club, you have the problem of how to handle it. I don't believe that we can completely get rid of it, but we can handle it fine."
Aubameyang, up for the 2017 African Player of the Year award, was also previously dropped for a Champions League game last year due to "internal reasons".