The vast majority of citation styles used by Authorea (over 9,000) are CSL styles (Citation Style Language) which are not BibTeX friendly. As such, if you pick one of these styles and export a LaTeX format of your document, you will get each citation encoded as \hyperref{}.

If you would like to get your citations exported in normal LaTeX/BibTeX mode, i.e. \cite{}, you need to pick a "BiBTeX" citation style before you export. How to find these styles? They include "(bibtex)" in their name, e.g. "IEEEtran (bibtex)", "Science (bibtex)", "apacite (bibtex)", etc. Pick one of these styles from the Export Options and export again.
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