Hmmm, I would really have expected "auto reverse" to be the culprit here as I can't think of any other way that a user could get this to happen "without them knowing/remembering" that they had caused it. For instance, though the batch could be copied with the "reverse entries" option ticked, this would have created a new batch and they would have had to post it and at some point in the process I think they would have realized that something was awry.
If they print batch listings check the header for the auto reverse status of the batch. Also, if memory serves me well, if the batch posted with the status enabled, this should mean that the original entries and the system generated auto reverse entries should be in the "same" posting journal.
I'm also remembering something about not being able to auto reverse in the last period of the fiscal year so bear that in mind as you troubleshoot.
Best regards, Pete