diff -u b/includes/bootstrap.inc b/includes/bootstrap.inc
--- b/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -1076,15 +1076,59 @@
   static $errors_triggered = array();
   if (empty($errors_triggered[$type][$name][$error_type])) {
     if ($error_type == 'missing') {
-      trigger_error(format_string('The following @type is missing from the file system: %name. In order to fix this, put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
+      _drupal_trigger_error_safe(format_string('The following @type is missing from the file system: %name. In order to fix this, put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
     }
     elseif ($error_type == 'moved') {
-      trigger_error(format_string('The following @type has moved within the file system: %name. In order to fix this, clear caches or put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
+      _drupal_trigger_error_safe(format_string('The following @type has moved within the file system: %name. In order to fix this, clear caches or put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
     }
     $errors_triggered[$type][$name][$error_type] = TRUE;
   }
 }
 
+/**
+ * Delays trigger_error() calls until Drupal has been fully bootstrapped.
+ *
+ * This is a Safe alternative for PHP's internal trigger_error().
+ * The Drupal error handler will add a watchdog message. Adding a watchdog
+ * message is not a safe operation before Drupal has been fully boostrapped.
+ * This function will delay trigger_error() calls until Drupal has been fully
+ * bootstrapped. If Drupal is already fully bootstrapped, this function will
+ * directly call the internal PHP trigger_error().
+ *
+ * @param $error_msg
+ *   The designated error message for this error. It's limited to 1024 bytes in
+ *   length. Any additional characters beyond 1024 bytes will be truncated.
+ * @param int $error_type
+ *   The designated error type for this error. It only works with the E_USER
+ *   family of constants, and will default to E_USER_NOTICE.
+ *
+ * @see trigger_all_queued_errors()
+ */
+function _drupal_trigger_error_safe($error_msg, $error_type = E_USER_NOTICE) {
+  if (drupal_get_bootstrap_phase() == DRUPAL_BOOTSTRAP_FULL) {
+    trigger_error($error_msg, $error_type);
+    return;
+  }
+
+  // It is not yet safe to trigger an error, so queue it up.
+  $errors = &drupal_static(__FUNCTION__, array());
+  $errors[] = array($error_msg, $error_type);
+}
+
+/**
+ * Calls a trigger_error() for all queued errors.
+ *
+ * @see trigger_all_queued_errors()
+ * @see _drupal_bootstrap_full()
+ */
+function _drupal_trigger_all_queued_errors() {
+  $errors = &drupal_static('_drupal_trigger_error_safe', array());
+
+  foreach ($errors as $error_parameters) {
+    call_user_func_array('trigger_error', $error_parameters);
+  }
+}
+
 /**
  * Writes the file scan cache to the persistent cache.
  *
diff -u b/includes/common.inc b/includes/common.inc
--- b/includes/common.inc
+++ b/includes/common.inc
@@ -2757,7 +2757,6 @@
   _registry_check_code(REGISTRY_WRITE_LOOKUP_CACHE);
   drupal_cache_system_paths();
   module_implements_write_cache();
-  drupal_file_scan_write_cache();
   system_run_automated_cron();
 }
 
@@ -2768,6 +2767,7 @@
   _registry_check_code(REGISTRY_WRITE_LOOKUP_CACHE);
   drupal_cache_system_paths();
   module_implements_write_cache();
+  drupal_file_scan_write_cache();
   system_run_automated_cron();
 }
 
@@ -5270,6 +5270,11 @@
     drupal_theme_initialize();
     module_invoke_all('init');
   }
+
+  // Execute all the delayed trigger_error()'s. Some errors are delayed because
+  // trigger_error() causes a watchdog call which is not a safe operation
+  // before Drupal is fully bootstrapped.
+  _drupal_trigger_all_queued_errors();
 }
 
 /**