diff -u b/modules/simpletest/tests/bootstrap.test b/modules/simpletest/tests/bootstrap.test
--- b/modules/simpletest/tests/bootstrap.test
+++ b/modules/simpletest/tests/bootstrap.test
@@ -414,18 +414,22 @@
     // Generate a non-existing module name.
     $non_existing_module = uniqid("", TRUE);
 
+    // We want to save that our anonymous error handler is triggered.
+    // This variable is inherited in the error handle with 'use'.
+    $get_filename_test_triggered_error = FALSE;
+
     // Searching for an item that does not exist returns NULL.
     // Set a custom error handler so we can ignore the file not found error.
-    set_error_handler(function($severity, $message, $file, $line) {
+    set_error_handler(function($severity, $message, $file, $line) use (&$get_filename_test_triggered_error) {
       // Skip error handling if this is a "file not found" error.
       if (strstr($message, 'is missing from the file system:')) {
-        cache_set('get_filename_test_triggered_error', TRUE);
+        $get_filename_test_triggered_error = TRUE;
         return;
       }
       throw new \ErrorException($message, 0, $severity, $file, $line);
     });
     $this->assertNull(drupal_get_filename('module', $non_existing_module), 'Searching for an item that does not exist returns NULL.');
-    $this->assertTrue(cache_get('get_filename_test_triggered_error'), 'Searching for an item that does not exist triggers an error.');
+    $this->assertTrue($get_filename_test_triggered_error, 'Searching for an item that does not exist triggers an error.');
     // Restore the original error handler.
     restore_error_handler();
     $this->assertNull(drupal_get_filename('module', $non_existing_module), 'Searching for an item that does not exist returns NULL.');
@@ -434,7 +438,7 @@
     $bad = &drupal_static('drupal_get_filename:missing');
 
     // Searching for an item that does not exist creates a static record in drupal_get_filename.
-    $this->assertTrue($missing['module'][$non_existing_module], 'Searching for an item that does not exist creates a static record in drupal_get_filename.');
+    $this->assertTrue($bad['module'][$non_existing_module], 'Searching for an item that does not exist creates a static record in drupal_get_filename.');
   }
 }
 
diff -u b/modules/system/system.admin.inc b/modules/system/system.admin.inc
--- b/modules/system/system.admin.inc
+++ b/modules/system/system.admin.inc
@@ -136,7 +136,7 @@
 function system_themes_page() {
   // Clean up the bootstrap "missing files" cache when listing themes.
   drupal_static_reset('drupal_get_filename:missing');
-  cache_clear_all('*', 'drupal_get_filename:missing', TRUE);
+  cache_clear_all('drupal_get_filename:missing', 'cache');
 
   // Get current list of themes.
   $themes = system_rebuild_theme_data();
@@ -794,7 +794,7 @@
 function system_modules($form, $form_state = array()) {
   // Clean up the bootstrap "missing modules" cache when listing modules.
   drupal_static_reset('drupal_get_filename:missing');
-  cache_clear_all('*', 'drupal_get_filename:missing', TRUE);
+  cache_clear_all('drupal_get_filename:missing', 'cache');
 
   // Get current list of modules.
   $files = system_rebuild_module_data();