The Monegasque had started 15th, one place behind runaway championship leader Verstappen, after both were hit with engine and gearbox-related penalties.
Leclerc pitted on lap three after complaining of overheating problems, with Ferrari then finding a tear-off strip lodged in his front right brake duct.
Binotto said the overheating had caused a sensor to fail which meant they could not measure Leclerc’s speed accurately when he made his final stop.
The five-second penalty for exceeding the speed limit dropped Leclerc one place to sixth.
"We were not using our normal sensors measuring the speed because they have been failed during the overheating... due to the (tear-off) of Max," Binotto told reporters at Spa-Francorchamps.
Leclerc made the late stop for fresh tyres so he could try and take a bonus point for fastest lap.
Instead, the stop briefly dropped him behind Alpine's Fernando Alonso.
Binotto said it had been worth the risk, even if Verstappen ultimately claimed the point.
"I think overall it has been an unlucky situation and we should not stop deciding to be brave to go for a fast lap when conditions are there to go for it," he said.
Leclerc, whose championship challenge has unravelled after reliability woes, driver errors and strategic missteps, is now 98 points behind Verstappen with eight races to go.
Drivers have layers of transparent ‘tear-off’ strips on their helmet visor that they peel off through the race to improve their visibility once dirty.
Verstappen had described Leclerc’s misfortune as "super-unlucky".
"I hope it’s not mine,” he added.
