In earlier chapters Hari has mentioned her and Eugene got really close in the previous timeline. It's been foreshadow that they've been attractive to each other in the previous timeline and the current. Iirc, it was mentioned before Hari isn't a mirror of their dead sister, but just has similar basic characteristics like the hair color. Also, it's been mentioned many times, especially with Eugene, they don't see her as a sister. As the others have said, they're close friends. If you don't like it, it's fine, but it's not incest and shouldn't be a shocking revelation that Hari and Eugene end up together. There's already been many hints that's the end game.