Having made last year's final, Atletico were big favourites against the out-of-form Leverkusen, but they lost 1-0 in the first leg of their last-16 match thanks to a stunning strike from Hakan Calhanoglu.
Simeone's team were outplayed by the Germans for the majority of the game and ended with 10 men after Tiago was sent off for a second bookable offence.
"It was a strange game, neither of the teams created that many chances," said Simeone.
"We had one at the end of the first half that we didn't manage to take and they had some in the second half. I'm happy, having made two changes in the first half, the disallowed goal, and we only lost 1-0. It could have been worse."