diff -r 53e2c979e4cd -r bc5148d0a446 mercurial/cmdutil.py
--- a/mercurial/cmdutil.py	Mon Jul 25 17:00:42 2016 +0200
+++ b/mercurial/cmdutil.py	Wed Jul 27 08:38:54 2016 +0000
@@ -2584,7 +2584,7 @@
     # Don't warn about "missing" files that are really in subrepos
     def badfn(path, msg):
         for subpath in ctx.substate:
-            if path.startswith(subpath):
+            if path.startswith(subpath + '/'):
                 return
         matcher.bad(path, msg)