The 1-1 result saw Arsenal bundled out of Europe 3-1 on aggregate.
Arsenal were only able to name six substitutes in Munich, with midfielder Ryo Miyaichi part of the travelling group following some late withdrawals, but it was later discovered he was not eligible for the pre-submitted Champions League squad.
"He was not eligible because he was not qualified to play in the Champions League because I wanted to give him out on loan, so we took him out of the list and UEFA informed us today that he is not qualified," said Wenger.
"Because he was on the bench on Saturday (against Everton), naturally he was with us but honestly that did not have an impact on tonight's result."
For breaking stories and all the great banter like us on Facebook: facebook.com/tribalfootball