Not sure if I'm looking at it right. If before the Anya/Jane fork counts, then I'm somehow missing an encounter with Naomi. If not, then I somehow got an extra point for Naomi when I went through Jane's run.
First did Anya path to the end. Then did Jane path at the fork to the end, skipping the "seen" dialog but selecting all the same choices and clicking on the glitches. When I got to the stats, I noticed that Naomi's number was a 3 for "all playthroughs". It counted her twice in the Jane run, but only once in the Anya run.
Edit: The "raw" counter is at 2 points in the Jane run, but the "potential" has only 1 point. On the Anya run, it's 1 and 1.
Accidentally edited out a part from above: After the scene with Naomi, I had to scroll back to click the clickable. I think I might've popped back into the choice at the end too (picked the top option each time).
Wish I could be more precise of what happened, but I wasn't looking for bugs and didn't notice the inconsistency until the very end.