I don't understand why he added a scene for Emily and John. Is he trying to turn the game into an NTR game? I wouldn't be surprised if he adds a shared scene with Melissa and John or the mc's girls soon. I'm starting to get bored of the game now.
As MC's mom is not an LI or pursuable in any way, is it really NTR? I get so confused with what does and doesn't qualify as that tag anymore; the definition doesn't always match where it is and isn't used. Some backers may have wanted to see Emily not be alone and forlorn anymore, and if you allow her to date John this may have been a way she allowed Emily to show she's getting back out into romance?
Melissa is expected to be a possible LI, so I would be surprised if she's fantasizing about the MC (on her path) she'd go out and be with another character in the game.
If you don't like the scene then skip it; or tell Emily you'd rather she didn't date John (she'll not date him, if you have enough Emily points).
Funny how one optional, and completely skippable scene completely ruins a game, but you do you.