--- a/Allura/allura/model/repo_refresh.py
+++ b/Allura/allura/model/repo_refresh.py
@@ -311,7 +311,8 @@
         last_commits = set(
             d['object_id']
             for d in last_commit_collection.find(
-                dict(object_id={'$in': rhs_tree_ids}),
+                dict(object_id={'$in': rhs_tree_ids},
+                     _id={"$regex": "^{}:".format(repo_id)}),
                 { 'object_id': 1, '_id': 0 }))
         for tree_id in rhs_tree_ids:
             if tree_id not in last_commits: