diff --git a/src/Plugins/Concerns/HandleArguments.php b/src/Plugins/Concerns/HandleArguments.php
index 9cf5e606a..beb80e384 100644
--- a/src/Plugins/Concerns/HandleArguments.php
+++ b/src/Plugins/Concerns/HandleArguments.php
@@ -44,16 +44,20 @@ public function pushArgument(string $argument, array $arguments): array
 
     /**
      * Pops the given argument from the arguments.
+     * Pops the given argument from the arguments and returns a re-indexed array.
      *
      * @param  array<int, string>  $arguments
      * @return array<int, string>
      */
     public function popArgument(string $argument, array $arguments): array
     {
-        $arguments = array_flip($arguments);
+        $key = array_search($argument, $arguments, true);
 
-        unset($arguments[$argument]);
+        if ($key !== false) {
+            unset($arguments[$key]);
+        }
+
+        return array_values($arguments);
 
-        return array_values(array_flip($arguments));
     }
 }
diff --git a/src/Plugins/Coverage.php b/src/Plugins/Coverage.php
index 712f5de55..5e2999611 100644
--- a/src/Plugins/Coverage.php
+++ b/src/Plugins/Coverage.php
@@ -17,6 +17,8 @@
  */
 final class Coverage implements AddsOutput, HandlesArguments
 {
+    use Concerns\HandleArguments;
+
     private const string COVERAGE_OPTION = 'coverage';
 
     private const string MIN_OPTION = 'min';
@@ -70,11 +72,9 @@ public function handleArguments(array $originals): array
             return false;
         }))];
 
-        $originals = array_flip($originals);
         foreach ($arguments as $argument) {
-            unset($originals[$argument]);
+            $originals = $this->popArgument($argument, $originals);
         }
-        $originals = array_flip($originals);
 
         $inputs = [];
         $inputs[] = new InputOption(self::COVERAGE_OPTION, null, InputOption::VALUE_NONE);