In the episode, Paolo (Rodrigo Santoro, pictured) and Nikki (Kiele Sanchez) are accidentally buried alive by their fellow castaways after being poisoned by venomous spiders.
The characters were introduced at the start of the current season but were widely loathed by fans for their late entrance.
"People hated them before they even opened their mouths to say anything significant because it felt like they were crashing the party," Lindelof told TV Guide.
"The easiest thing would have been to just write them out and forget they ever happened, like the cougar on [Season 2] of 24. But that's not Lost. We should at least own up to it."
Sanchez, meanwhile, was unfazed by the criticism but admitted her final scenes were tough. "I am horribly claustrophobic - I can't even have a blanket over my face - so I didn't have to do a lot of acting," she recalled. "I was genuinely terrified."
Lost continues this Sunday at 10pm on Sky One.