Its hard to find good ones on that. There are some like "Scars of Summer" which have hints and narrative twists that can be seen by the male character, the (very popular) "behind the curtain" / unknown identity twist where the FMC behaves suspiciously by you can not 100% pin it down. Henteria Chronicles (pixel-art inspired by NTRPG) does this too. The more recent "Nebel Geisterjäger" does also have somewhat hidden NTR where you encounter the scenes that happened only after you go to sleep. You basically dream of them in some kind of dream/alternate reality realm. Although its a bit more obvious there and unfortunately the open world/free roam town lacks interactions that make you really enjoy these events happening (outside of the CG unlock).