User scripts have headers containing @-prefixed directives just like this does, including one which is named @include — this (obviously) causes trouble when attempting to use this for user scripts (which is one of the most applicable uses of this)
Not sure how to fix, except maybe ignore things within the UserScript header block.
That kind of sucks. You have a code sample? Not sure what the best way around that would be without some hacks or annoying edge case logic.