"F" or "UF" key missing in file specification

It could be fonts but I really don't know what is causing it other than something occured during InDesign saves. However, the error can be cleared using Acrobat Professional, Print Production, Pre Flight.

Select single fixups (wrench icon), and depending on the version of Professional, you may need to select, Acrobat Pro DC 2015 prfiles from the drop-down within the dialog box for Preflight. Selecting this opens a lot more options. Look under the Document category for, INsert missing F and UF entries for embedded files; then use the Fix button.

A file specification can be used in a number of different places in a PDF, so without knowing more, it's hard to say what's wrong. It could be related to an embedded file, a link to an external file, a launch file action, a submit form action, import form data action, etc.