diff -r cb4b0ec54990 -r 9350f00a7b23 mercurial/exchange.py
--- a/mercurial/exchange.py	Tue Nov 03 12:15:14 2015 -0800
+++ b/mercurial/exchange.py	Tue Nov 03 12:16:54 2015 -0800
@@ -1658,6 +1658,10 @@
     if not repo.ui.configbool('experimental', 'clonebundles', False):
         return
 
+    # Only run if local repo is empty.
+    if len(repo):
+        return
+
     if pullop.heads:
         return