Each story map has a one to one mapping with an agile board. If you are missing issues on the story map it is good to check they are also present on the backlog of the agile board.
In this case, the missing issues may be excluded due to one of these reasons:
* This is due to the required step of mapping Statuses to Status Categories not being performed after upgrading from a version of JIRA released prior to the introduction of Status Categories
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