Hello LWW -
This is not especially unusual for items submit to eBay. If eBay's product catalog (which can, on occasion, be in error and if it is you can report that to eBay) shows your product in a category other than the one you select when you go to list, their system will change the category to the one it finds most appropriate. Their system will make determinations regarding your product by the unique identifiers such as ISBN and then assign a category it finds most appropriate.
Based on your comment here, it sounds like there are cases for you where eBay has inappropriate information for your product and in such cases you will need to let eBay know by providing them the example of your product and they should be able to make updates on their end with that information.