Just wanted to reiterate this because I'm not totally sure what's up either, but I think that at least for some of the events where you're intended to lose relationship points (leaving the orphanage, leaving Yureyu), you actually end up GAINING the points. I haven't looked at the code myself, all I've done is just compare the relationship points after doing certain events. I'm also not sure if this is just isolated to the events where you leave an area after being partnered with somebody or if it's the negative RP events in general.
Also, I think beating Aya on the first try grants