As the programme was broadcast, the BBC took the extraordinary step of confirming their crews had taken action to stop and help.
"Every turtle that was seen or filmed by the Planet Earth II crew was collected and put back into the sea," a spokesman for the show told fans on Twitter.
Previously, nature documentary-makers have been firm on the importance of crews keeping a distance from the animals they are filming.
Sir David said last year: "If you're a film cameraman you are trained, as it were, to be the observer, a non-participant. That's very important."
Doug Allan, a cameraman behind some of the most famous wildlife scenes in television history, has said: "For me, at least, my job is to look and not interfere. If I feel my presence is tilting the balance of the predator or the prey, then I'm doing something wrong."
A BBC source said that in this instance, the problem was man-made and it was therefore appropriate for man to step in to assist.
Sir David's programmes have previously come under fire for filming dying animals, with a particularly emotional outpouring after an elephant calf died of thirst.
Speaking about the scenes depicted in the documentary series Africa last year, the broadcaster admitted: "The worst thing in this series as far as I'm concerned was that poor little baby elephant dying of thirst.
"Of course you see really tough things, but there's nothing you can do about them."
He said camera crews and wildlife presenters would "actually make things far worse by responding than not", adding that it was "very important" to simply observe.
Planet Earth II, which is reaching record-breaking numbers of viewers, has already tugged on the heartstrings of fans with soaring music, emotional scenes and a barrage of social media reaction each week.
After the final episode, in which Sir David explored the impact of the man-made world on the animal kingdom, social media was flooded with emotional messages about the baby turtles and their plight.
The BBC later released a short film documenting the work of a special task force at the Barbados Sea Turtle Project, who collect lost turtles and put them back on course to the sea.