Don't start it again, please...
I just wanna weigh in cause dear lord I'm sick of these NTR arguments
From Wikipedia, "Cheating or being unfaithful to a significant other, lit. "taken away by sleeping with", abbreviated NTR"
This presents
two requirements;
One, this means that the partner is unfaithful.
Traditionally, this means that a marital relationship had extramarital relationships.
But within the context, it's mostly referencing a sexual relationship wherein a romantic partner does not consent to the sexual activity their partner engages in.
In short, cheating on your romantic partner.
This does not apply to the universe of Subverse, because there are no romantic relationships, or individual romantic relationships hinted or stated in the story.
Secondly, it requires exclusivity between partners.
Obviously, there is no exclusivity within the crew. Everyone is "free game", including the monsters, tentacles, and whatever other things that Lily has in her lab.
I bet that if that male anal play was better accepted by most people that the captain would even be involved with tentacles in some sort of Lily Tentacle Experiment something scene.
TL;DR: The crew within the story don't have any relationships or exclusivity, therefore NTR is not applicable.