diff --git a/src/Configuration/ConfigurationFactory.php b/src/Configuration/ConfigurationFactory.php
index 902b0ec7..4497e6df 100644
--- a/src/Configuration/ConfigurationFactory.php
+++ b/src/Configuration/ConfigurationFactory.php
@@ -265,7 +265,10 @@ private function retrieveExcludedFiles(string $dirPath, array $config): array
                 $file = $dirPath.DIRECTORY_SEPARATOR.$file;
             }
 
-            $excludedFiles[$index] = realpath($file);
+            unset( $excludedFiles[$index] );
+            $fileKey = str_replace( $dirPath.DIRECTORY_SEPARATOR, '', $file );
+            $file = realpath($file);
+            $excludedFiles[$fileKey] = $file;
         }
 
         // We ignore files not found excluded file as we do not want to bail out just because a file we do not want to
@@ -353,7 +356,7 @@ private static function retrieveFilesWithContents(iterable $files): array
     {
         $filesWithContents = [];
 
-        foreach ($files as $filePathOrFileInfo) {
+        foreach ($files as $fileKey => $filePathOrFileInfo) {
             $filePath = $filePathOrFileInfo instanceof SplFileInfo
                 ? $filePathOrFileInfo->getRealPath()
                 : realpath($filePathOrFileInfo);
@@ -366,7 +369,7 @@ private static function retrieveFilesWithContents(iterable $files): array
                 throw InvalidConfigurationValue::forUnreadableFile($filePath);
             }
 
-            $filesWithContents[$filePath] = [$filePath, file_get_contents($filePath)];
+            $filesWithContents[$fileKey] = [$filePath, file_get_contents($filePath)];
         }
 
         return $filesWithContents;
diff --git a/src/Console/ConsoleScoper.php b/src/Console/ConsoleScoper.php
index ed237d5b..70b0bfb1 100644
--- a/src/Console/ConsoleScoper.php
+++ b/src/Console/ConsoleScoper.php
@@ -255,10 +255,10 @@ private static function getFiles(Configuration $config, string $outputDir): arra
 
         $commonDirectoryPath = self::getCommonDirectoryPath($config);
 
-        $mapFiles = static fn (array $inputFileTuple) => new File(
+        $mapFiles = static fn (array $inputFileTuple, string $fileKey ) => new File(
             Path::normalize($inputFileTuple[0]),
             $inputFileTuple[1],
-            $outputDir.str_replace($commonDirectoryPath, '', Path::normalize($inputFileTuple[0])),
+            $outputDir.str_replace($commonDirectoryPath, '', Path::normalize($fileKey)),
         );
 
         return [
@@ -266,13 +266,15 @@ private static function getFiles(Configuration $config, string $outputDir): arra
                 array_map(
                     $mapFiles,
                     $filesWithContent,
-                ),
+                    array_keys( $filesWithContent )
+                )
             ),
             array_values(
                 array_map(
                     $mapFiles,
                     $excludedFilesWithContents,
-                ),
+                    array_keys( $excludedFilesWithContents )
+                )
             ),
         ];
     }