Do you have bots blocked in your settings? It could be bot posts that aren't being shown; they still show up on post counts and reply numbers (and your notifications).
Oh maybe that's it, good idea. Do you know where that setting is? I must be blind today because I know I've seen it before but now I can't find it...
Upper right corner, click your username -> Settings, scroll all the way to the bottom.
I don't block bots but I still have this problem. Something else is causing it.
Sometimes these are comments that were deleted. I deleted a comment of my own and it showed up in a thread that way
This is the true answer. It can verified by using other apps or the lemmy-ui (official instance website)