Chief executive Hans-Joachim Watzke has claimed that Aubameyang 'withheld' performances after it emerged that the Gunners were interested in his signature.
However, Wenger has suggested that Aubameyang's physical condition may have had something to do with his below-par display against Freiburg.
At a press conference, the Frenchman told reporters: "If you look well at the history, he played only one game. He played, they suspended him for two or three games.
"One before the [winter] break and one after the break. So he played only one game at home, where they played a 2-2.
"So maybe he was not ready physically to perform at his best, but I don't believe that he didn't want to perform."
Aubameyang made his debut for Arsenal in the 5-1 win over Everton last weekend, with the Gabon international getting on the scoresheet before half time at the Emirates Stadium.