Index: src/applications/repository/engine/PhabricatorRepositoryRefEngine.php
===================================================================
--- src/applications/repository/engine/PhabricatorRepositoryRefEngine.php
+++ src/applications/repository/engine/PhabricatorRepositoryRefEngine.php
@@ -304,8 +304,9 @@
     $all_commits = queryfx_all(
       $conn_w,
       'SELECT id, commitIdentifier, importStatus FROM %T
-        WHERE commitIdentifier IN (%Ls)',
+        WHERE repositoryID = %d AND commitIdentifier IN (%Ls)',
       $commit_table->getTableName(),
+      $repository->getID(),
       $identifiers);
 
     $closeable_flag = PhabricatorRepositoryCommit::IMPORTED_CLOSEABLE;
Index: src/applications/repository/storage/PhabricatorRepository.php
===================================================================
--- src/applications/repository/storage/PhabricatorRepository.php
+++ src/applications/repository/storage/PhabricatorRepository.php
@@ -592,6 +592,10 @@
       return false;
     }
 
+    if (!$this->shouldTrackBranch($branch)) {
+      return false;
+    }
+
     return $this->isBranchInFilter($branch, 'close-commits-filter');
   }