City missed out on top place in Group D of the Champions League after an astonishing gaffe by Pellegrini.
City beat the European champions 3-2 at the Allianz Arena but Pellegrini did not realise that a fourth goal would have kept his side away from the likes of Real Madrid and Barcelona in the knockout stage.
Pellegrini admitted that he would only have put on Aguero if City had made it 4-2.
"Maybe if we had scored a fourth goal I would have made the change," said the confused Chilean coach. "It was important to be first in the group but not the most important.
"Arsenal on Sunday was a priority above this game. I said it was very difficult to win by three goals."
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