Scuderia drivers Sebastian Vettel and Charles Leclerc were held up by each other during the race, having been split on strategy mid-race.
Leclerc got stuck behind fourth-placed Vettel in the opening stint after the German picked up a flatspot in the first corner, before they swapped positions on Lap 12.
Vettel joined the Mercedes and Red Bulls on a two-stop strategy, taking service for the first time at the end of Lap 19, and found himself being held up when Leclerc resumed from his initial stop after Lap 25, on a harder tyre compound.
That situation lasted a dozen laps until the Monegasque driver was instructed to move aside for Vettel.
“Should have we swapped earlier? I think it is never an easy decision but we as a team are trying to optimise our performance and team result at the end,” said Binotto.
“We've swapped in the past and tried to swap again today as they were on a different strategy at that stage.
“Should have we done it earlier? I think by the time you do it you need to know if the driver behind has the faster pace, otherwise you are swapping and not having any result. It may take a few laps to assess that.
“On the other side (second stint), Charles was fighting for third place with Verstappen because he was on a different strategy with the hard tyres, a single pit stop, so it was important for him not to lose any lap time at that stage of the race.
“We simply waited for the right moment and should we do it again, I am not sure if we should have done it earlier.”
Vettel went on to finish fourth, about 1.5s back from Max Verstappen, while Leclerc, who did end up in the pits a second time with 20 laps remaining due to a Safety Car, was fifth.
Mercedes continued its streak of one-two results and now heads Ferrari by 96 points in the constructors' championship, with Binotto admitting that the upgrades it took to the Circuit de Barcelona-Catalunya did not deliver as hoped.
The next round is the Monaco Grand Prix on May 23-26.