What is it?
"Milestones" are how Logos resources are organized; if you type a reference into the reference box (at the top-left of a resource panel), you're navigating to that milestone within the resource. Logos 6 introduces "{Milestone <Reference>}" search syntax to find these milestones in search results.
How does it work?
While <John 3:16> finds all references to John 3:16, {Milestone <John 3:16>} finds all instances of John 3:16; these could be that verse in a Bible, or a discussion of that verse in a commentary. (This search basically returns the same results as the Commentaries section in the Passage Guide.)
You can use any reference supported by the resources in your library; for example, {Milestone <ApostolicFathers I Clement 1>} finds all texts that include 1 Clem 1.