Why are Zotero citations or bibliographies always highlighted in gray or another color?

By default, Zotero stores the reference data for citations and the bibliography in Fields (Word) or Reference Marks (LibreOffice), which stores items' reference data hidden behind the formatted text.

Word and LibreOffice will highlight Fields/Reference Marks on your screen to indicate that the text is automatically generated. This can help you avoid accidentally manually typing in the fields (to edit the text shown in a Zotero citation, see Customizing Cites). These highlights are only shown on screen and won't appear if you print or save the document as a PDF.

You can change the settings for highlighting Fields/Reference Marks in your word processor:

See also Citations Highlighted.