diff --git a/src/Configuration/ConfigurationFactory.php b/src/Configuration/ConfigurationFactory.php
index 10dbdf81..e56b5bec 100644
--- a/src/Configuration/ConfigurationFactory.php
+++ b/src/Configuration/ConfigurationFactory.php
@@ -293,7 +293,10 @@ 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;
         }
 
         return array_filter($excludedFiles);
@@ -390,7 +393,7 @@ 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);
@@ -413,7 +416,7 @@ private static function retrieveFilesWithContents(iterable $files): array
                 );
             }
 
-            $filesWithContents[$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 a8e1a722..a32bd1f7 100644
--- a/src/Console/ConsoleScoper.php
+++ b/src/Console/ConsoleScoper.php
@@ -178,20 +178,22 @@ private static function getFiles(Configuration $config, string $outputDir): arra
         );
         Assert::notNull($commonDirectoryPath);
 
-        $mapFiles = static fn (array $inputFileTuple) => [
+        $mapFiles = static fn (array $inputFileTuple, string $fileKey ) => [
             Path::normalize($inputFileTuple[0]),
             $inputFileTuple[1],
-            $outputDir.str_replace($commonDirectoryPath, '', Path::normalize($inputFileTuple[0])),
+            $outputDir.str_replace($commonDirectoryPath, '', Path::normalize($fileKey)),
         ];
 
         return [
             array_map(
                 $mapFiles,
                 $filesWithContent,
+                array_keys( $filesWithContent )
             ),
             array_map(
                 $mapFiles,
                 $excludedFilesWithContents,
+                array_keys( $excludedFilesWithContents )
             ),
         ];
     }