The Ecuador coach believes referee Noumandiez Doue's performance will be examined by his superiors after a number of key decisions went against his side at the Maracana
The South Americans held les Bleus despite being reduced to 10 men on 50 minutes when Manchester United winger Antonio Valencia was dismissed for a high challenge on Lucas Digne.
But their resistance proved in vain as Switzerland convincingly dispatched Honduras 3-0 in Manaus to wrap up second spot in Group E and set up a round-of-16 clash with Argentina.
For Rueda, Valencia's dismissal was compounded by Doue's failure to sanction Mamadou Sakho after the Liverpool defender appeared to elbow Oswaldo Minda in the head in a scrappy first half.
"It's quite regrettable," Rueda admitted when asked about the incident. "This is now in the hands of the committee that assesses the behaviour of referees.
"There was not the ideal behaviour in many split decisions but it's not really worth going into now.
"Everything that happened is quite unfortunate. I'm very respectful of the referees and it's water under the bridge.
"We lost an important man in our structure - maybe the most important for his experience - we suffered and the game ended as it did. Faced with France, it was very difficult to hold the result."
Rueda's contract as Ecuador coach has now expired, but he insists he is keen to continue in the role.
"Now my contract concludes and it will be assessed by the federation in Ecuador to make decisions for the future," he added. "It seems to me that we did a great job.
"We renewed the team - it was a significant renewal - and it's the best heritage we have for the next four to eight years, depending on how we look after these players."