I think it is about the save counts.
I tested a few things, the bug seems to occur so far after a certain number of saves.
So far I tried :
- Completing the game 100% with no saving require (with and without the help of the debug room). The glitch didn't occur
- Doing a normal run (30~50 saves) the glitch didn't occur
- Doing the game with as many saves possible, the glitch happened and past 150 saves, I couldn't talk to any NPC anymore
- Booting a new game and saving repeatedly a the start, I got the same results as previously
I have noticed a few glitchs with the birth mecanics as well, but they are unrelated and you really have to screw with it to get them.