As the film was being finished up, producer Roger Corman felt that the picture needed more sex, nudity and monster shots throughout, so he ordered scenes shot that showed the humanoids attacking and ripping the clothes off of other nubile young women. Director Barbara Peeters, who was a feminist who hated that idea, refused to shoot the scenes. Corman said he'd hire a second director and get her feedback before using the new footage. She agreed to that. But Corman ended up never showing the new footage to her or the cast and other crew. They didn't see them until the preview of the film. Peeters was furious, protesting that they were inserted purely to show gratuitous nudity. Corman also edited out many of the scenes dealing with the plot and character development in order to make room for the nudity and more creature scenes. Peeters complained that it was no longer the film she made and wanted her name taken off. Corman said he'd do that but only if she paid the expense of redoing the credits. She wouldn't, so her name stayed on the project. Many years later, Peeters ended up watching the film on cable and admitted it actually ended up being "a fun little movie."
Actress Ann Turkel once said why she chose to do this film: "It was an intelligent suspenseful science-fiction story with a basis in fact and no sex". It also had the title "Beneath The Darkness" that she loved. However, then Corman not only added more scenes of graphic nudity and monster rape, he also changed the title to Humanoids from the Deep, which Turkel hated.
There are only three Humanoid creatures seen together on-screen in the same frame throughout the movie. The production really only had one fully functioning Humanoid costume and two others that could only be shot from certain angles because they weren't as convincing. Use of such angles, as well as the editing, would help to create the illusion that there were much more Humanoids than just three for the climactic carnival massacre.
Director Barbara Peeters once said that the "humanoids" were originally suppose to be played by the film's stunt men. Unfortunately, the stunt men found the monster suits to be too "goofy-looking" and refused to wear them. Additional actors had to be hired to perform as the monsters.
One scene of the Humanoids attacking a naked female victim on the beach was shot when the temperature was cold enough to turn the actress's lips blue. The make up team kept having to make her lips pink again.