Visma-Lease a Bike rider Yates was visibly frustrated after finishing 24 seconds behind Del Toro in seventh.
“The plan was completely different from what we did today, so I will talk about that with the team,” he told Eurosport.
“I will not say anything more about that.”
However, team director Marc Reef said the day went “exactly as we agreed”, and added Carapaz and Del Toro were “just a bit stronger”.
Although Yates, 32, could still overhaul Carapaz and Del Toro, it looks most likely this year will again add to the heartbreak he has experienced in bids to win the Giro.
He led for 13 days in 2018 but cracked in the final week when Chris Froome launched an astonishing comeback to win the race.
After an underwhelming eighth-placed finish in 2019, Yates had to withdraw from the 2020 edition with Covid-19 and then had to recover from a difficult first two weeks to claim third in 2021.
Yates’ twin brother Adam sat up and dropped out of the top 10 overall in order to save himself to help team-mate Del Toro on Saturday.
Ecuador’s Carapaz, the 2019 Giro champion, tried to drop Del Toro on the final climb, but could not shake the 21-year-old, who is bidding to become the youngest winner of the Giro since 1940.
UAE Team Emirates-XRG rider Del Toro, who won stage 17, showed impressive nous to grab the six bonus seconds for second place, with EF Education-EasyPost’s Carapaz, 32, having to settle for four bonus seconds in third.
