The sending-off of captain Antonio Valencia for a dangerous challenge on Lucas Digne left the South American nation to play most of the second half with 10 men, while an apparent elbow by Mamadou Sakho on Oswaldo Minda in the first half was missed by Ivorian referee Noumandiez Doue.
"What happened was a shame. It is up to the committee that looks after these things to judge the performance of the referee," said Rueda of the latter incident. "A lot of his 50-50 decisions were not ideal."
However, the Colombian did appear to accept the sending-off of Valencia, saying: "It is a shame, but I am very respectful and what happened has happened. There is nothing to be done about it now.
"We lost an important player in our structure and it was difficult to hold on for a draw but thanks to the character of the players we did so."
Rueda, who led Honduras to the 2010 finals in South Africa, is now out of contract but he declared his hope that an agreement can be found with the Ecuadorean Football Federation (FEF) for him to stay at the helm.
"Now my contract is up and it is up to the Federation to decide over my future. I think we have done a good job."