I just remembered an important thing. Co-sleeping which is the norm in Japan.
Maybe Niina was always in parents' bed, if it is the cultural norm?
Or, the opposite could have been true, the room where Rei used to sleep that night, was usually Niina's one?
Would it be possible that the perpetrator expected it to be Niina's room, and it was Rei there, and that's what went astray?
I don't remember the second child room on that floor, and tbh, having read about co-sleeping practice in Japan eons ago, I assumed Niina always slept upstairs...but what if they alternated, or indeed, the killer didn't know whose bedroom it was?
ETA: usually it would be expected that the younger kid may be cosleeping, right? But Rei had some developmental issues, perhaps he had enuresis, too. Then a younger boy sleeping alone would be expected...but the perpetrator might have not known it. He attacked women way worse...