In the Versions pane of Plan view (JIRA Agile Scrum board), we get all versions from all projects instead of just the versions for the primary project for this board. What dictates what versions are listed in that pane? Of note, no issues from the other projects are present on the board.
Make sure your filter query has the project criteria in it. If it is generic, the board assumes that you want to show issues from all project and that will pull in versions from all projects in to the board.
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