Lewandowski, who is widely expected to join the European champions when his contract expires in a year's time, said after the weekend Supercup 4-2 win over Bayern that he was happy still to be a Dortmund player as he gets on well with his team-mates - but not so much with certain other members of the club.
Watzke told the Bild newspaper that such a feeling was to be expected.
"Obviously he's referring to me," he said. "But I have got to make decisions for the good of this club.
"I can fully accept that Robert is a bit frustrated."
Dortmund have also received offers from other European clubs for the Poland striker, but the player has his heart set on joining Bayern and has turned down a move to any other club and is now expected to see out the final year on his contract with Dortmund.