I have Endnote X8 installed with Word 2016 on OSX.
I often view documents using “Smart Markup”.
When Endnote formats the citations in a document it switches the view from “Smart Markup” to “All Markup”.
This is a bug.
I understand that Endnote is perhaps doing something behind the scenes related to track changes, and needs to temporarily switch modes. I imagine that given that “smart markup” is a relatively new view in Word on OSX, that perhaps the code has not been updated to reflect this status and then restore the view to this state.
Endnote should record the actual markup view that was active prior to formatting references. I hope that in future versions of Endnote that this is corrected.
If anyone knows of a work around I would be happy to hear about it.