It's okay to add NTR if:
-It happens at the beginning of the game as part of the storyline (this is the storyline NTR, which players didn't truly know the girlfriend, it can be because the game starts after it happened already or just at the beginning and being an important part of the game story, such as revenge or payback).
-It happens as a consequence when you fail to achieve something or you ignore a problem for a long time (for example games in which you party with female characters and if defeated they may be captured and raped by monsters, another point would be when a character is interested in your girlfriend and you don't kick his ass).
-It is an open relationship or some weird shit within it.
It isn't okay to add it if:
-It is unavoidable at a later point in the story, unless it is a mainly NTR themed game, in that case go nuts for the fans if you want.
-It depends on player's actions that were totally unclear the effects of it.
-The game focus is absolutely unrelated to NTR and it wasn't originally planned to happen.
Overall NTR can be a point of conflict and serve as a point to generate a storyline, be it save a character before it's too late, competition with other characters, or as a point to make the MC want to eliminate another character.