The Poland international had been hoping to move to Bundesliga champions Bayern Munich during the close-season, but Dortmund refused to sell the striker, and he is now expected to move to the Allianz Arena on a free transfer in 12 months' time.
Juergen Klopp's side defeated their rivals 4-2 in the DFL Super Cup on Saturday, and though Lewandowski failed to score, he put in an impressive performance.
He maintains he has no problems representing Dortmund, but the 24-year-old has revealed he is unhappy with certain personnel outside of the playing squad.
"When I am on the pitch, I want to play well and score goals," he told Sky Deutschland.
"That is the most important thing for me, no matter where I play.
"I feel fine in the team, but with other people I do have a problem. That is a difficult issue."
Dortmund general manager Hans-Joachim Watzke conceded he was the likely target of the striker’s ire, but insisted decisions had been made in the best interest of the team.
Watzke explained to Bild: "Obviously he's referring to me but I have got to make decisions for the good of this club.
"I can fully accept that Robert is a bit frustrated."
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