Just ran into this same issue.
I have various custom post types available for a relationship field, but one CPT is being ignored on save.
As this remains the thread that ranks in search engines for “Reusable field group ACF”, it might be nice to mention the following here:
Version 5.4 will include a new “Clone” field.
– From John Heubner’s preliminary work on https://github.com/Hube2/acf-reusable-field-group-field
See: https://www.advancedcustomfields.com/resources/clone