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1 custom taxonomy registered for 2 different CPT (custom post type). When i entered to edit tag section on edit-tags.php?taxonomy=mytaxonomy&post_type=cpt1 it displays total post count of 2 different CPT. Is there any way to fix that?

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This is a known issue see Custom taxonomy count includes draft & trashed posts. It might not be fixed in version 3.2 but most likely in the next version.

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