I believe there is a bug when having 2 custom taxonomies having the same categories. I.e
Custom_post type A => TaxonomyA
TaxonomyA_categories => Blake, James, David, Phil;
Custom_post_type B = > TaxonomyB
TaxonomyB_categories => Blake, Davis, Charles, Craig
When Changing the category Black in Custom_Post_type B it will also change the category in custom_post_type A as well.
Even if you have 2 separate post types and taxonomies they must be named differently or else you will run into this problem.
Any Suggestions on trying to fix it?