This was reported on bug 20641 comment #10 and confirmed by me:
$ php maintenance/namespaceDupes.php --wiki=zhwiki --fix
Looks good!
$ sql zhwiki
mysql> SELECT COUNT(*) FROM archive WHERE ar_namespace=0 AND ar_title LIKE 'CAT:%';
+----------+
| COUNT(*) |
+----------+
| 41 |
+----------+
1 row in sec (0.00 sec)
Version: 1.16.x
Severity: enhancement