Norwegian referee Svein Oddvar Moen booked Burak Yilmaz, for allegedly diving in the penalty area, and will now miss the second leg through suspension.
And Inan believes his side did not get the rub of the green in the Spanish capital.
“His decisions helped Madrid. He made many errors. The yellow card for Burak (Yilmaz) was a mistake,” he told AS.
“We had a lot of bad luck. We were very disappointed with the match. [Atletico Madrid's] Arda Turan told us how to play Madrid, but the result gives them a great advantage.”
The midfielder has not given up all hope of qualifying for the semi-finals despite needing to win by four goals to go through.
However if his side do get knocked out he would like Los Blancos to go on to become champions.
“Everything is possible in football. It's difficult for us to win 4-0, but we are Galatasaray and we'll try to do our best, to win and show we are a strong team," he added.
“They are a great club, and they are candidates to win the trophy. If we don't qualify I want Madrid to win the Champions League. If they do win it, we'll be able to say we were knocked out by the champions.”