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..515a572bbd 100644
--- a/src/Standards/Generic/Tests/PHP/BacktickOperatorUnitTest.php
+++ b/src/Standards/Generic/Tests/PHP/BacktickOperatorUnitTest.php
@@ -43,8 +43,8 @@ public function getErrorList()
      */
     public function getWarningList()
     {
-        // Warning about incorrect annotation will be shown on line 1 once PR #3915 would be merged.
-        return [];
+        // Warning about incorrect annotation.
+        return [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,
diff --git a/tests/Core/ErrorSuppressionTest.php b/tests/Core/ErrorSuppressionTest.php
index 725a1e59d9..5b5ac471e7 100644
--- a/tests/Core/ErrorSuppressionTest.php
+++ b/tests/Core/ErrorSuppressionTest.php
@@ -501,15 +501,15 @@ public function dataNestedSuppressLine()
 
             // Process with line suppression nested within disable/enable suppression.
             'disable/enable: slash comment, next line nested single line suppression'         => [
-                'before' => '// phpcs:disable'.PHP_EOL.'// phpcs:ignore',
+                'before' => '// phpcs:disable'."\n".'// phpcs:ignore',
                 'after'  => '// phpcs:enable',
             ],
             'disable/enable: slash comment, with @, next line nested single line suppression' => [
-                'before' => '// @phpcs:disable'.PHP_EOL.'// @phpcs:ignore',
+                'before' => '// @phpcs:disable'."\n".'// @phpcs:ignore',
                 'after'  => '// @phpcs:enable',
             ],
             'disable/enable: hash comment, next line nested single line suppression'          => [
-                'before' => '# @phpcs:disable'.PHP_EOL.'# @phpcs:ignore',
+                'before' => '# @phpcs:disable'."\n".'# @phpcs:ignore',
                 'after'  => '# @phpcs:enable',
             ],
         ];
@@ -671,7 +671,7 @@ public function dataSuppressFile()
             'ignoreFile: start of file, hash comment, with @'         => ['before' => '# @phpcs:ignoreFile'],
             'ignoreFile: start of file, single-line star comment'     => ['before' => '/* phpcs:ignoreFile */'],
             'ignoreFile: start of file, multi-line star comment'      => [
-                'before' => '/*'.PHP_EOL.' phpcs:ignoreFile'.PHP_EOL.' */',
+                'before' => '/*'."\n".' phpcs:ignoreFile'."\n".' */',
             ],
             'ignoreFile: start of file, single-line docblock comment' => ['before' => '/** phpcs:ignoreFile */'],
 
@@ -752,18 +752,18 @@ public function dataDisableSelected()
                 'expectedErrors' => 1,
             ],
             'disable: single sniff, docblock'              => [
-                'before'         => '/**'.PHP_EOL.' * phpcs:disable Generic.Commenting.Todo'.PHP_EOL.' */ ',
+                'before'         => '/**'."\n".' * phpcs:disable Generic.Commenting.Todo'."\n".' */ ',
                 'expectedErrors' => 1,
             ],
             'disable: single sniff, docblock, with @'      => [
-                'before'         => '/**'.PHP_EOL.' * @phpcs:disable Generic.Commenting.Todo'.PHP_EOL.' */ ',
+                'before'         => '/**'."\n".' * @phpcs:disable Generic.Commenting.Todo'."\n".' */ ',
                 'expectedErrors' => 1,
             ],
 
             // Multiple sniffs.
             'disable: multiple sniffs in one comment'      => ['before' => '// phpcs:disable Generic.Commenting.Todo,Generic.PHP.LowerCaseConstant'],
             'disable: multiple sniff in multiple comments' => [
-                'before' => '// phpcs:disable Generic.Commenting.Todo'.PHP_EOL.'// phpcs:disable Generic.PHP.LowerCaseConstant',
+                'before' => '// phpcs:disable Generic.Commenting.Todo'."\n".'// phpcs:disable Generic.PHP.LowerCaseConstant',
             ],
 
             // Selectiveness variations.
@@ -780,17 +780,17 @@ public function dataDisableSelected()
 
             // Wrong category/sniff/code.
             'disable: wrong error code and category'       => [
-                'before'           => '/**'.PHP_EOL.' * phpcs:disable Generic.PHP.LowerCaseConstant.Upper,Generic.Comments'.PHP_EOL.' */ ',
+                'before'           => '/**'."\n".' * phpcs:disable Generic.PHP.LowerCaseConstant.Upper,Generic.Comments'."\n".' */ ',
                 'expectedErrors'   => 1,
                 'expectedWarnings' => 1,
             ],
             'disable: wrong category, docblock'            => [
-                'before'           => '/**'.PHP_EOL.' * phpcs:disable Generic.Files'.PHP_EOL.' */ ',
+                'before'           => '/**'."\n".' * phpcs:disable Generic.Files'."\n".' */ ',
                 'expectedErrors'   => 1,
                 'expectedWarnings' => 1,
             ],
             'disable: wrong category, docblock, with @'    => [
-                'before'           => '/**'.PHP_EOL.' * @phpcs:disable Generic.Files'.PHP_EOL.' */ ',
+                'before'           => '/**'."\n".' * @phpcs:disable Generic.Files'."\n".' */ ',
                 'expectedErrors'   => 1,
                 'expectedWarnings' => 1,
             ],
@@ -1047,7 +1047,7 @@ public function dataIgnoreSelected()
                 'expectedWarnings' => 1,
             ],
             'disable: single sniff; ignore: single sniff' => [
-                'before'           => '// phpcs:disable Generic.Commenting.Todo'.PHP_EOL.'// phpcs:ignore Generic.PHP.LowerCaseConstant',
+                'before'           => '// phpcs:disable Generic.Commenting.Todo'."\n".'// phpcs:ignore Generic.PHP.LowerCaseConstant',
                 'expectedErrors'   => 1,
                 'expectedWarnings' => 0,
             ],