This sounds really interesting. I've never seen the crimson butterfly in Rei's house myself, but I know that there are a lot of well-hidden little secrets in this game, so I see no reason not to believe you. I once discovered something with a friend, and we literally spent hours trying to find out what triggered it. I'll describe it again here (I mentioned it on the old forums before), since it may help understand how some seemingly insignificant details can be important in triggering stuff like this.
So, here goes (late game SPOILERS):
At the time, we were nearing the end of the game and had just done the final battle against Crawling Woman and Rope Priestess. We then did some more random exploration and also left the Manor of Sleep (meaning, we woke up to heal because we were out of Herbal Medicines) a couple of times. Then, one time, there was a voice coming from the spirit radio when we woke up. I believe it's Yoshino's voice, or maybe Crawling Woman's. Anyway, we were kind of creeped out because this was new to us, and so we went to explore Rei's house to see if we could find the source of the voice. When we left Rei's room, the voice stopped. Still, we explored the entire house to make sure. When we reached the room with Yuu's shrine, there was a moaning sound coming from the closet in the corner, but when we opened it, nothing was there. We reloaded to check again, but aside from the moan, there was nothing to be seen/heard anywhere.
I'll spare you the description of how exactly we found out what to do in order to trigger this, and just explain what the triggers are. Keep in mind that it's been a long time since I played FF3, so I hope I remember everything correctly. First, it's important to take Crawling Woman's picture (it's called Trapped Woman) when you find her inside the closet in the Futon Room. Fight her, then wake up. Develop the film, then give the picture to Miku for research. Go to sleep, then wake up again and collect the new info on Crawling Woman from Miku. Now, go to sleep again, and then wake up AGAIN, and you will hear the voice coming from the radio. Go downstairs to the corner in the room with Yuu's shrine to hear the moan. That's it, from what I recall. Also, this cannot be done anymore once you reach the next chapter.
What makes this so unlikely to be discovered is that you have no reason to wake up again after getting that info from Miku. I know this isn't directly related to the butterfly, but maybe the butterfly's criteria are similar. Just a thought^^"
Anyway, I'll definitely try to help with finding the trigger for this butterfly scene, since I'm really curious about it:)