diff --git a/src/Psalm/Plugin/EventHandler/Event/AfterAnalysisEvent.php b/src/Psalm/Plugin/EventHandler/Event/AfterAnalysisEvent.php
index 92ac8ae9b79..60db94732b0 100644
--- a/src/Psalm/Plugin/EventHandler/Event/AfterAnalysisEvent.php
+++ b/src/Psalm/Plugin/EventHandler/Event/AfterAnalysisEvent.php
@@ -10,7 +10,7 @@ final class AfterAnalysisEvent
 {
     private Codebase $codebase;
     /**
-     * @var IssueData[][]
+     * @var array<string, list<IssueData>> where string key is a filepath
      */
     private array $issues;
     private array $build_info;
@@ -19,7 +19,7 @@ final class AfterAnalysisEvent
     /**
      * Called after analysis is complete
      *
-     * @param array<string, list<IssueData>> $issues
+     * @param array<string, list<IssueData>> $issues where string key is a filepath
      * @internal
      */
     public function __construct(
@@ -40,7 +40,7 @@ public function getCodebase(): Codebase
     }
 
     /**
-     * @return IssueData[][]
+     * @return array<string, list<IssueData>> where string key is a filepath
      */
     public function getIssues(): array
     {
diff --git a/src/Psalm/Plugin/Shepherd.php b/src/Psalm/Plugin/Shepherd.php
index bb0ba7bb1da..49dc628e9b3 100644
--- a/src/Psalm/Plugin/Shepherd.php
+++ b/src/Psalm/Plugin/Shepherd.php
@@ -120,11 +120,11 @@ private static function collectPayloadToSend(AfterAnalysisEvent $event): ?array
             return null;
         }
 
-        $issues = $event->getIssues();
-        $normalized_data = $issues === [] ? [] : array_filter(
-            array_merge(...array_values($issues)),
+        $issues_grouped_by_filename = $event->getIssues();
+        $normalized_data = $issues_grouped_by_filename === [] ? [] : array_values(array_filter(
+            array_merge(...array_values($issues_grouped_by_filename)), // flatten an array
             static fn(IssueData $i): bool => $i->severity === IssueData::SEVERITY_ERROR,
-        );
+        ));
 
         $codebase = $event->getCodebase();