For example the file anchor on this revision:
https://secure.phabricator.com/D18465#change-cv4o_.vkNhKk
When using the remarkup to link to it, the period prevents the full anchor from being used.
D18465#change-cv4o_.vkNhKk
The link will still navigate to the revision, it just won't jump to the linked file.
See also T12970#234322