I too am running into this problem, it is maybe not so rare... unfortunately it hits you when you least need it (grant deadline).
In my case I am using Linux, LibreOffice 5.2.4.2 and Zotero standalone. I am using bookmarks as I have to share the document with users that use Word (however the current document I have has not been edited in word at all).
I experience the same problem: when inserting some citations (or editing existing ones with the zotero edit citation button) I get asked the Yes/No question for a lot of the references (but not all curiously). After I say NO (because I think Yes means that the reference will not longer be updated and I need to be sure the numbers move up when I add a citation before), the reference gets duplicated. For example "Smith et al.13" becomes "Smith et al.1313".
Even worse, after a number of times of this happening now it is recognizing the references in the wrong place. Now it started highlighting pieces of text that had no reference (like two characters in the middle of a word), and substituted those characters by the reference. This completely messes up everything. In one case it substituted 3 lines of text for the new reference. (yes I have backup all the time).
This is a serious bug, even if it is rare. (does not seem so rare to me).
I also develop scientific software so I know that you need help debugging this. I will be able to help, but only after my deadline tomorrow (with this bug it's looking like I will need a sleepless night).
Thanks so much. For this reason, I am only using Zotero now for the first reference of a source, to maintain a running bibliography for my dissertation. For all other footnotes, I insert the reference the "old-fashioned" way--by hand, per Chicago style. Much faster, and free from bugs.
I have now switched to using ReferenceMarks, rather than Bookmarks. This meant re-entering all my references (120 by now). The problem has not reappeared yet. It may be that the bug is related with using bookmarks for zotero references?
Of course, the problem of using ReferenceMarks is that I cannot share the document with Word users...
As the preferences say, Bookmarks are a lot more fragile, so I could see this happening more easily (e.g. with a simple change in formatting). It's also a lot more easy for the to capture surrounding text, so yes, I'd try to stay away from them in long-ish document as much as possible (and if need be switch only before converting to .doc and .odt).
If people get us anything resembling steps to (consistently) reproduce this, we'd certainly be happy to take a look. Without that, it's kind of hard.
Upgrade Storage
In my case I am using Linux, LibreOffice 5.2.4.2 and Zotero standalone. I am using bookmarks as I have to share the document with users that use Word (however the current document I have has not been edited in word at all).
I experience the same problem: when inserting some citations (or editing existing ones with the zotero edit citation button) I get asked the Yes/No question for a lot of the references (but not all curiously). After I say NO (because I think Yes means that the reference will not longer be updated and I need to be sure the numbers move up when I add a citation before), the reference gets duplicated. For example "Smith et al.13" becomes "Smith et al.1313".
Even worse, after a number of times of this happening now it is recognizing the references in the wrong place. Now it started highlighting pieces of text that had no reference (like two characters in the middle of a word), and substituted those characters by the reference. This completely messes up everything. In one case it substituted 3 lines of text for the new reference. (yes I have backup all the time).
This is a serious bug, even if it is rare. (does not seem so rare to me).
I also develop scientific software so I know that you need help debugging this. I will be able to help, but only after my deadline tomorrow (with this bug it's looking like I will need a sleepless night).
Thank you
Of course, the problem of using ReferenceMarks is that I cannot share the document with Word users...
If people get us anything resembling steps to (consistently) reproduce this, we'd certainly be happy to take a look. Without that, it's kind of hard.