I had the same problem. I couldn’t identify fhe style that Word 2016 was using – the style of the reference list matched none of the styles available in the document. The only solution was to convert to unformatted citations, create a new version of the file – thankfully, it was a short one – with no formatting (i.e. paste special, text only). The bulleting disappeared when the citations were updated. Then I had to put the formatting back in the new file. The document used a lot of bulleted lists, and EndNote was clearly picking this up in some way that made no sense.