Every time, I try to add citations, I get the message "Zotero experienced an error updating your document. Would you like to view troubleshooting instructions?"

I have re-started word and zotero, updated my word, turned off track changes with no help.

You should follow the steps on the troubleshooting page all the way to the end, but submitting a Report ID after having received the error message since restarting Zotero might help us troubleshooting. What word processor are you using?

I also have a separate issue where my document with zotero citations inserted 2 subsequent bibliographies at the bottom of the text, with numbers attached to my paper's in-text references. I can't delete the second bibliography as it will unlink the references in my text.

Removing the bibliography from your document doesn't unlink any citations. You can remove both bibliographies and use the Add/Edit Bibliography button in the Zotero tab to reinsert a fresh bibliography. However, if you have manually added any items to the bibliography via the Edit Bibliography dialog in the past, those will not be reinserted. Generally in your case you can remove one of the two bibliographies and the remaining one should continue working and updating with citations in the document.