diff --git a/src/Rule/Rules/File/PhpFileFinder.php b/src/Rule/Rules/File/PhpFileFinder.php
index 5d60fe53..ee271900 100644
--- a/src/Rule/Rules/File/PhpFileFinder.php
+++ b/src/Rule/Rules/File/PhpFileFinder.php
@@ -9,6 +9,7 @@
 use Boundwize\StructArmed\File\SkipPathMatcher;
 use Boundwize\StructArmed\Util\Path;
 
+use function array_keys;
 use function array_unique;
 use function array_values;
 use function is_dir;
@@ -66,37 +67,39 @@ public function filesFromScope(
         array $scopeFiles,
         array $skipPaths = [],
     ): array {
-        $sourcePaths     = $this->sourcePaths($basePath);
-        $filesByPath     = [];
-        $skipPathMatcher = SkipPathMatcher::compile($basePath, $skipPaths);
+        $skipPathMatcher   = SkipPathMatcher::compile($basePath, $skipPaths);
+        $directoryPrefixes = [];
+
+        foreach ($this->sourcePaths($basePath) as $sourcePath) {
+            $directoryPrefixes[] = Path::normalise(Path::resolve($sourcePath, $basePath), canonicalise: true) . '/';
+        }
 
-        foreach ($scopeFiles as $file) {
-            $file = Path::normalise($file, canonicalise: true);
+        $files = [];
+
+        foreach ($scopeFiles as $scopeFile) {
+            $scopeFile = Path::normalise($scopeFile, canonicalise: true);
 
-            if (! str_ends_with($file, '.php') || $skipPathMatcher->isSkipped($file)) {
+            if (isset($files[$scopeFile])) {
                 continue;
             }
 
-            $filesByPath[$file] = $file;
-        }
-
-        $files = [];
+            if (! str_ends_with($scopeFile, '.php')) {
+                continue;
+            }
 
-        foreach ($sourcePaths as $sourcePath) {
-            $resolvedSourcePath = Path::resolve($sourcePath, $basePath);
-            $directoryPrefix    = Path::normalise($resolvedSourcePath, canonicalise: true) . '/';
+            if ($skipPathMatcher->isSkipped($scopeFile)) {
+                continue;
+            }
 
-            foreach ($filesByPath as $file) {
-                if (! str_starts_with($file, $directoryPrefix)) {
-                    continue;
+            foreach ($directoryPrefixes as $directoryPrefix) {
+                if (str_starts_with($scopeFile, $directoryPrefix)) {
+                    $files[$scopeFile] = true;
+                    continue 2;
                 }
-
-                $files[] = $file;
-                unset($filesByPath[$file]);
             }
         }
 
-        return $files;
+        return array_keys($files);
     }
 
     /** @return list<string> */
diff --git a/tests/Rule/File/PhpFileFinderTest.php b/tests/Rule/File/PhpFileFinderTest.php
index e39027ee..29cdf38a 100644
--- a/tests/Rule/File/PhpFileFinderTest.php
+++ b/tests/Rule/File/PhpFileFinderTest.php
@@ -109,4 +109,18 @@ public function testEachFinderFiltersScopeUsingItsOwnSourcePaths(): void
             (new PhpFileFinder(['custom/']))->filesFromScope($basePath, $scopeFiles),
         );
     }
+
+    public function testIgnoresDuplicateScopeFiles(): void
+    {
+        $basePath = $this->makeTemporaryDirectory('structarmed-php-file-finder');
+        mkdir($basePath . '/src');
+
+        $sourceFile = $basePath . '/src/Foo.php';
+        file_put_contents($sourceFile, '<?php');
+
+        $this->assertSame(
+            [Path::normalise($sourceFile, canonicalise: true)],
+            (new PhpFileFinder(['src/']))->filesFromScope($basePath, [$sourceFile, $sourceFile]),
+        );
+    }
 }