The scene appears without any explanation and shows Captain James T Kirk checking out Carol Marcus in her underwear.
Abrams told Conan O'Brien that the moment was in line with Kirk's womanising character. He, however, admitted that perhaps he didn't quite edit "the scene in the right way."
Film's co-writer Lindelof agreed the scene looked like it was unwarranted.
"We also had Kirk shirtless in underpants in both movies. Do not want to make light of something that some construe as misogynistic. What I'm saying is I hear you, I take responsibility and will be more mindful in the future," he added.
Eve, 31, also addressed the controversy, saying, "I think the nature of what we do is visual and so all of us are subject to typecasting.
"I think J J Abrams very carefully and decidedly walks the line between allowing audiences to have what they expect from cinema, which is to have these paradigms but also to try to slightly adjust tired stereotypes.