Henrik Frisk <frisk.h@gmail.com> writes:

>> Hmm. Did you customize `org-src-fontify-natively'?
>>
>
> This is what I have:
>
> (setq org-confirm-babel-evaluate nil
>       org-src-fontify-natively t
>       org-src-tab-acts-natively t)

Then, might be https://debbugs.gnu.org/cgi/bugreport.cgi?bug=63579
If it is, putting (defvar font-lock-reference-face nil) into your config
should help; and, ideally, also reporting the bug to lilypond devs.