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. (Agencies)
"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,” he added.
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,” he added.
The result combined with Switzerland's 3-0 success against Honduras left Ecuador as the first South American nation to be knocked out of this World Cup.
Ecuador had beaten Honduras 2-1 in their second game last Friday but Rueda admitted that their prospects of qualifying for the last 16 were compromised when they lost by the same scoreline to Switzerland in their opening match in Brasilia.
"We didn't play at our very best against Switzerland and didn't take our chances when they came," said the 57-year-old.
Enner Valencia put Ecuador ahead in that game only for Admir Mehmedi to equalise before Haris Seferovic struck an injury-time winner that ultimately proved crucial.
"In that first game we needed to play with greater freedom. Switzerland are an experienced and well-organised team who did very well in qualifying. It was either them or us,” he said.
Switzerland now go on to face Argentina in the last 16, leaving Ecuador as the only CONMEBOL nation to fall short at the group stage.
They came through qualifying without winning a single away game and their overall performances in Brazil confirmed that they are not the same team away from the altitude of their home in Quito.
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,” he said.
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.