The winger was given a three-match ban following the red card he was shown in the first leg of their semi-final against Lyon for a tackle on Lisandro Lopez.
The German club failed in an appeal to UEFA and have now turned to the Court of Arbitration for Sport, who will deliver a verdict on May 18.
Mourinho said: "It's strange, really strange.
"Everybody knows why he saw the red card. I don't know, what can they have?
"And because of Busquets the referee made a mistake and so Motta cannot play in the final when he did nothing to see the red card.
"We didn't appeal because we understand the rules of the game but I don't understand why Bayern did it but we concentrate on ourselves.
"We have a final in Siena and after that we have a final in Madrid."