diff --git a/src/Files/File.php b/src/Files/File.php
index 03ed0c14aa..984de785bd 100644
--- a/src/Files/File.php
+++ b/src/Files/File.php
@@ -879,6 +879,7 @@ protected function addMessage($error, $message, $line, $column, $code, $data, $s
         // Filter out any messages for sniffs that shouldn't have run
         // due to the use of the --sniffs command line argument.
         if ($includeAll === false
+            && $parts[0] !== 'Internal'
             && ((empty($this->configCache['sniffs']) === false
             && in_array(strtolower($listenerCode), $this->configCache['sniffs'], true) === false)
             || (empty($this->configCache['exclude']) === false
diff --git a/src/Standards/Generic/Tests/PHP/BacktickOperatorUnitTest.php b/src/Standards/Generic/Tests/PHP/BacktickOperatorUnitTest.php
index f3e8cfd537..7cc77f7bdc 100644
--- a/src/Standards/Generic/Tests/PHP/BacktickOperatorUnitTest.php
+++ b/src/Standards/Generic/Tests/PHP/BacktickOperatorUnitTest.php
@@ -43,8 +43,10 @@ public function getErrorList()
      */
     public function getWarningList()
     {
-        // Warning about incorrect annotation will be shown on line 1 once PR #3915 would be merged.
-        return [];
+        return [
+            // Warning about incorrect annotation.
+            1 => 1,
+        ];
 
     }//end getWarningList()
 
diff --git a/src/Standards/Generic/Tests/PHP/DisallowAlternativePHPTagsUnitTest.php b/src/Standards/Generic/Tests/PHP/DisallowAlternativePHPTagsUnitTest.php
index be242c781d..cef051b481 100644
--- a/src/Standards/Generic/Tests/PHP/DisallowAlternativePHPTagsUnitTest.php
+++ b/src/Standards/Generic/Tests/PHP/DisallowAlternativePHPTagsUnitTest.php
@@ -56,7 +56,15 @@ public function getErrorList($testFile='')
     public function getWarningList($testFile='')
     {
         if ($testFile === 'DisallowAlternativePHPTagsUnitTest.2.inc') {
+            // Check if the Internal.NoCodeFound error can be expected on line 1.
+            $option = (bool) ini_get('short_open_tag');
+            $line1  = 1;
+            if ($option === true) {
+                $line1 = 0;
+            }
+
             return [
+                1 => $line1,
                 2 => 1,
                 3 => 1,
                 4 => 1,
diff --git a/src/Standards/Generic/Tests/PHP/DisallowShortOpenTagUnitTest.php b/src/Standards/Generic/Tests/PHP/DisallowShortOpenTagUnitTest.php
index 3edda9a567..625122984d 100644
--- a/src/Standards/Generic/Tests/PHP/DisallowShortOpenTagUnitTest.php
+++ b/src/Standards/Generic/Tests/PHP/DisallowShortOpenTagUnitTest.php
@@ -88,7 +88,14 @@ public function getWarningList($testFile='')
         case 'DisallowShortOpenTagUnitTest.1.inc':
             return [];
         case 'DisallowShortOpenTagUnitTest.3.inc':
+            // Check if the Internal.NoCodeFound error can be expected on line 1.
+            $option = (bool) ini_get('short_open_tag');
+            $line1  = 1;
+            if ($option === true) {
+                $line1 = 0;
+            }
             return [
+                1  => $line1,
                 3  => 1,
                 6  => 1,
                 11 => 1,