The problem could be related to how you register the custom post type.
Did you add the “taxonomies” argument in the register_post_type? If yes, is it a string? Try to convert it in an array of strings.
See the the example below…
register_post_type(
'custom_post_type_slug',
array(
'labels' => array ( /* ... */ ),
'public' => true,
/* ... */
'taxonomies' => array( 'custom_post_taxonomy_slug' ),
)
);