...viewing your product lists in your admin and under status will be a green box(active) and next to it a yellow box(linked)
Take note of the product ID - view the linked product and take note of the master category
If it is not the category you are viewing - then it is linked from elsewhere and you can delete it
To make this easier, you can install Admin Master Link Icon from Plugins. This makes the icon orange for the master category version of the linked product, and yellow for linked category versions. No need to go into each product and view the list and compare categories.