Steps to Recreate:

1. Create Demo Site
2. Install Flag Module and Bookmark Sub-module
3. View /posts/your-first-post - No bookmark
4. Go to /admin/structure/flags/manage/bookmarks and check box "Display on Full content view mode"
5. View /posts/your-first-post - See that bookmark is visible
6. Go to /admin/structure/types/manage/post/display/default to change the placement of bookmark flag, but don't see any option.
7. Go to /admin/structure/flags/manage/bookmarks and check box "Display link as field"
   
8. Go to /admin/structure/types/manage/post/display/default and see that you can now change the placement of the flag/bookmark.
9. Go to /posts/your-first-post and see that the flag is showing up twice.

The steps above happened to me and it took me about 20 minutes to figure out that you MUST check either "Display on Full content view mode" OR "Display link as field", but you should NOT check both - or this will happen to you.

I was convinced I had found a bug, but now realize it's just confusing UI.

I'm thinking about ideas for making this better now and hope to submit a PR.