This is almost certainly because you have messages from users that you have blocked or bot users and you have disabled seeing bot accounts. I believe that if you hit the mark all read button, even the nonvisible messages should be marked as read.
if you visit https://lemmy.world/api/v3/user/unread_count (in a signed-in session) you can see where these numbers are coming from.
if you could share these numbers in a pm to me i can take a look at where the difference may be coming from.
it would also be useful which 2 messages you are seeing, at least the type of them (pm, mention, reply).
There is only a single link. If you're currently using an app you might need to do this from a browser.
Im on a laptop using firefox can't you investigate it? I will log out so you can use my account to see what the problem is.
We'll never login to your account and never ask you for your password.
We can check these things in a different way, but it would save time to just have this information provided by you, so we can see which area to look at. The notification number in the top right takes 3 different numbers as inputs and only shows the sum of all of them, and each one of them has different logic working behind it.
Just kind of seems like I got all these messages I can't reply to beside the two that I have saved. But am willing to give up my account to you just so you can correct whatever is wrong.
I believe I found the root cause, as you have configured your account not to show bot accounts.
the lemmy version used on lemmy.world does not currently filter those out, even though they are not shown in the actual message view.
this was fixed for a newer lemmy version already, but it should be a rather simple backport.
i've put it on my list of potential backports.
meanwhile you can try enabling showing bot accounts in your account settings and you should see all those messages. feel free to disable it again afterwards.
If you're using an app, check the other tabs (mentions and direct messages). It might be that you have some of those and not simply replies to comments/posts you've made, which is usually the default page on most apps when you go to the inbox.