Index: wp-admin/includes/class-wp-upgrader.php
===================================================================
--- wp-admin/includes/class-wp-upgrader.php	(revision 28024)
+++ wp-admin/includes/class-wp-upgrader.php	(working copy)
@@ -431,11 +431,13 @@
 			$this->skin->feedback('maintenance_start');
 			// Create maintenance file to signal that we are upgrading
 			$maintenance_string = '<?php $upgrading = ' . time() . '; ?>';
-			$wp_filesystem->delete($file);
+			if( is_file( ABSPATH . '.maintenance' ) ) {
+				$wp_filesystem->delete($file, false, 'f');
+			}
 			$wp_filesystem->put_contents($file, $maintenance_string, FS_CHMOD_FILE);
-		} else if ( !$enable && $wp_filesystem->exists($file) ) {
+		} else if ( !$enable && is_file( ABSPATH . '.maintenance' ) ) {
 			$this->skin->feedback('maintenance_end');
-			$wp_filesystem->delete($file);
+			$wp_filesystem->delete($file, false, 'f');
 		}
 	}