This happens if you click the "flag" button on a deleted post when you don't have enough reputation to see deleted posts, but you still see it because your browser loaded the page before the post was deleted, and you haven't refreshed the page to reflect the recent deletion. In other words, it's almost like a caching issue on your end.
This has happened to me often when I'm reviewing first posts, when I get a review item that isn't deleted but deserves deletion, and I load the flag dialog. After I load it and select an option, the post is deleted just moments before I actually click the "Flag [Question|Answer]" button. When that happens, I get an error message saying something like:
You don't have permission to flag this post.
Then, if I try to load the flag dialog again, it appears just like how you describe, with only the custom flag option.
I know that the post is deleted when I go into my recent review items and go to the review task, where I see that the post is "not found".