Pitching in my frustration - upgraded to Endnote X8 last weekend. Mac OS was updated from .5 to .6 (Sierra (10.12.6) two days ago.
Now I’ve gone from a few crashes a day to crashes every hour. My library of data is in a non-cloud service folder (username/endnote). Interestingly I see that Spotlight sees the pdf folder, so now I’ve added the data folder into the privacy area to prevent spotlight from indexing the pdfs. I’ll let you know how that goes, after I reboot the system completely.