if you open https://lemmy.world/api/v3/user/unread_count after being logged in, it should at least tell you what kind of unread message it is.
with that information it can probably be narrowed down a bit.
i don't think this is related to an inconsistency with blocked users, as that is only being fixed in 0.19.4 or 0.19.5: https://github.com/LemmyNet/lemmy/issues/4227
moderated or deleted comments as mentioned by others don't look like they would be the case when i'm looking at the 0.19.3 code.
the bot reply mentioned by @[email protected] seems like a very plausible explanation, as bot accounts are hidden from the comment reply list in the api, but they're not currently excluded from the notification count.
i'll have a look at whether that is still the case in the current development version in a bit and submit a pr to fix that if it is.