How to stop (ii) being converted to a reference

It sounds like you have changed your bibliography layout settings or preferences to use regular parentheses rather than the default curly brackets as your endnote temporary delimiters.  

You can change as in the the attached image for the document you are working on. Image 1

You should change it in the peferences (on a PC you edit from the Edit menu, on a Mac, I think it is under the “apple” menu).  see image 2