add flag to product display view
I am having the same problem. It seems like there is no way to add 'flag' relationship in view used by facets.. 
The way I have done this is:


I installed the module 'Views PHP'
(https://drupal.org/project/views_php) 
Added a 'global PHP'
field in my faceted view. 
called the function to create flag
link and printed the link in the global php field: print flag_create_link('bookmarks', $data->entity)


Dont know why, my php view cudn't render $row->nid, thus I used $data->entity for node id.

Remember to enable php filter once views php is installed.

Hope It helps.