Basically the same issue as this one: http://tracker.moodle.org/browse/MDL-30144 except for version 2.3.
I narrowed this down to the assign::get_all_submissions function: http://pastebin.com/UuvMBT70 . The comments indicate that it should return all submissions by ENROLLED students, but the SQL doesn't look at enrolled users. Here's a patch I came up with: http://pastebin.com/jmPKZ4z2 . I based it heavily off of the user filtering found in the assign_grading_table class (in mod/assign/gradingtable.php).