Duplicated message in a mail box could append when consolidating to mailbox or only by mistake. Since each message is identified by an unique message-id while sending, duplicated message have the same message-id, and therefore can be easily identified.
To identify them with mutt, you need to configure it to thread duplicated
messages together when sorting by threads. This is done through the
duplicate_threads configuration variable. If active, the duplicated messages
will be marked with an = in the thread diagram.
To activate it, put in your .muttrc the following line:
set duplicate_threads = yes
or type in mutt :set duplicate_threads = yes. To check if it is active, type in mutt :set ?duplicate_threads.
Know to identify the duplicated messages you can use the ~= pattern and use it
for marking or deleting them.
For example to tag all the duplicated messages type T for tagging according to
a pattern and then ~= to select the duplicated messages in the folder. If you
want to delete them use D for deleting according to a pattern and then ~= to
select the duplicated messages in the folder.