Ishii felt Sergio Ramos deserved to be sent off late on with the game in the balance.
"We have created problems for Real Madrid, but these matches are resolved by small differences, such as decisions of players or techniques," he began.
"My players from the match were brave and played at their best. But the referee perhaps at a particular time was not brave enough, and I think that is regrettable."
Asked if he was referring to the Ramos incident, the coach added: "I don't want to go too far..."