Reinaldo Rueda says Ecuador "suffered" after Antonio Valencia's red card against France as they exited the World Cup.
The South Americans were still in with a reasonable chance of qualifying for the last 16 as they entered the second half of their clash with Les Bleus at the Maracana on Wednesday night.
However, Manchester United winger Valencia was then sent off by Ivory Coast referee Noumandiez Doue just five minutes after the restart for a lunge on left-back Lucas Digne, leaving Rueda's men with an even tougher task.
Even then, they had chances to nick a victory while goalkeeper Alexander Dominguez performed heroics at the other end to keep the scoresheet blank. Elsewhere, Switzerland's 3-0 win over Honduras in Manaus put the European side through as runners-up.
Rueda said: "It is quite unfortunate everything that happened. I am very respectful of the referees and these issues are water under the bridge - there is nothing to be done.
"We lost an important man and we suffered from it.
"It's quite unfortunate some of the decisions made by the referee did not favour us but that's in the hands of the people who have to analyse the performance of the referee."
Rueda admitted that his side's opening match against Switzerland, when Ecuador conceded the winning goal in injury time, had proved critical.
He added: "This has been a short tournament for us, we paid the price for that first match when we lost against Switzerland."