ml2json is quite chatty about what it's doing. It has multiple importance levels:
a NOTE level which is only shown when specifying the --verbose option and used to tell about normal decisions and may explain reasons for how the conversion is being done,
a WARN level that is used for cases when it worries that something done in the conversion may not be right,
__WARN__ is used whenever Perl or some third party library issues a warning itself
ERROR when there was an exception while handling a message or mailbox; the exception is captured, i.e. didn't lead to the abort of the whole conversion process, but means that the part of the conversion that's indicated in the context of the ERROR (usually one message, or one mailbox file during mbox parsing) is skipped. Unless the input is clearly faulty (corrupt mbox files, for example), this is probably an indication of a bug, please report.
(I may add a --quiet option that silences WARN and __WARN__)
In all cases after the level indicator there is an indication of the context in which the issue has happened, which is either an "identify" value (see message identification) or something other possibly useful.
NOTE[/run/shm/chris/ml2json/b1946ac92492d2347c6235b4d2611184/0/__meta]: unknown message with messageid '591785b794601e212b260e25925636fd@abc.com' given in in-reply-to header of b1946ac92492d2347c6235b4d2611184/0 at lib/Chj/Ml2json/Mailcollection.pm line 173
This means that none of the mbox files that were read by ml2json contained any message with message-id 591785b794601e212b260e25925636fd@abc.com. This would typically happen if someone sends a reply to a mailing list email privately, i.e. using the "reply" instead of "reply to all" function in their mailer, and then the receiver of that reply sending a reply back to the list (by manually re-adding the mailing list address). The first reply is then never making it to the archive, but the second is, while having a in-reply-to header that lists the mail that was private.
It could also happen if the first reply was actually sent to the list, but not archived for some reason. Actually with NNTP (Usenet news) there is a "X-No-Archive" header that people can set so that their message is distributed to the public but not archived on the servers; perhaps some mailing list software respects that as well.