I have created a table of contents and am using a total of 3 layers within
it. There are a few duplicate entries, i.e the same layer listed twice with
the same page.

There is only one instance of this section, so I am not sure what is going
on. I have changed it to Body Text, updated the table, which removes it,
then place it back as a layer 3 and update the table, and the duplicate
entries are still there.

Any suggestions?