Import problem with categories and custom taxonomies

First – a bit of background:
I am working with a new client on integrating a WP blog (located in a /blog/ subdirectory) into the existing site (also built on WP). The reason it was setup that way was to allow posts to be used for an extensive image gallery. Rebuilding this gallery was the primary project and I used CPTs and custom taxonomies. It is working great and now there are a total of 0 posts, so we decided to import the blog to eliminate administrative headache.

Second – the actual problem
I exported the posts and categories from the blog install using export and WP import plugin. It worked fine, but I am getting a new auto gen category for each post in one single category. All the other categories are OK.

Third – what I was able to find out
There is a custom taxonomy with the same name as that category, but as far as I can tell I should be able to duplicate slugs in different taxonomies. At least that is how it handled other categories with matching slugs. It seems they used the same wp_term and created a new wp_term_taxonomy.

It isn’t a huge issue to change the slug of the taxonomy, but I want to prevent future issues and category archives ending in random integers. And even more so, I am desperately curious about what caused the problem. Especially considering it only happened to one single category.