I think this is going to be a pretty difficult one to figure out!
Sometimes, when viewing my INBOX (at least; perhaps other folders
too) and selecting a mail to view in the pager, the wrong mail is
displayed in the pager. It's a mail from the same thread (I think
this only happens with messages in threads), possibly (but I have
not confirmed this) always an 'adjacent' mail.
A consequence of this, when it happens, is I'm really hesitant to
delete mails, since I can't be sure I will be deleting the right
messages.
My config: invoke neomutt via an alias m=neomutt. I'll attach all
my config files to this email or a follow-up. (Sorry, they are a
mess). I use neomutt with IMAP.