Hi,
i believe that i found an issue in the last release FLEXIcontent v3.2.1 (11/09/2017)
When you edit an entry with two categories affected.
If you try to delete the secondary categories in Assignements table, when you save and close, the secondary category is not deleted.
To circumvent this, you can affect the same secondary category as the main category.
Then, when you save with main category and secondary category identical, you obtain secondary category empty.
Could someone test this and confirm this issue?