The Atleti coach witnessed his side wilt at the Bernabeu on Wednesday, with own goals from Emiliano Insua and Miranda coming either side of Jese Rodriguez's strike.
It means Atletico face an uphill task in the second leg at the Vicente Calderon, as the club look to defend the title they won last season against Real.
Simeone remains confident his side can progress, however, but lamented their inability to create opportunities.
"We have 90 minutes more, this is football and we have 90 minutes more to play," he said.
"Real Madrid played a really good game and we have to congratulate them for how they played.
"We had (Diego) Godin's chance to reduce the difference. We gave a big effort but couldn't find the ways to make more chances.
"It's a really good result for our rival."
