Did you take Yuka's Charm? That's a factor in the "Naomi takes Yuka to the restroom" route.
I FIGURED IT OUT! So the save file should be tracking the deaths properly, but I messed up on the order of the characters in the ending screen. So the game knows you've gotten the ending where Yoshiki is the only dead character, but it's listing as though you have the ending where only Ayumi dies in its place. So the ending you're ACTUALLY missing is the one where Ayumi is the only death.
I'll make a quick patch to fix this, but you should be able to just kill Ayumi in the Science Lab and complete that ending list. Sorry for the confusion, and again, thank you for bringing this to my attention! Feedback like this helps us solo devs improve our games!