Some of my categories are hidden and can't be deleted

This is a strange bug I’m getting.

Here’s what I did: I am creating a website for a bird-watching station and they want to keep a species database of all the birds they’ve seen. They had it set up as categorized posts and when I took over, I decided to convert all the posts to a custom post type called “species” and take the information from their categories and input them as custom fields.

An example:

The White Crowned Parrot
Class Aves
Order Psittaciformes
Family Psittacidae
Genus Pionus
Species Pionus senilis (Spix, 1824)
Spanish Name Loro de Corona Blanca

So their categories were set up hierarchically, with “Psittaciformes” as a subcategory of “Aves”, etc.

I created a new post type called “species” using Custom Post Type UI (http://wordpress.org/extend/plugins/custom-post-type-ui/). Which does not have categories. I used the plugin Post-Type Switcher (http://wordpress.org/extend/plugins/post-type-switcher/) to switch existing posts to species.

So far so good.

Now I have a strange problem that all these categories (Aves, etc) are still showing up when you go to Posts > Filter by Category. However, if you select one, it says no posts found. If you click on Categories, these categories don’t show up at all, but it says there is a second page of categories that turns up blank.

I thought that the Convert Categories to Tags plugin might help me, so I installed that, and it tells me “Convert Categories (32) to Tags” and then underneath that it only shows 10 Categories (the ones I should have).

I would like to delete these phantom categories as I no longer have any use for them. But I can’t delete them the normal way. Can anyone provide an explanation about what’s going on or maybe provide suggestions as to what I can do? Thanks!