diff --git a/scanpullrequest/scanpullrequest.go b/scanpullrequest/scanpullrequest.go
index 1282f37ce..e01f3b0c3 100644
--- a/scanpullrequest/scanpullrequest.go
+++ b/scanpullrequest/scanpullrequest.go
@@ -170,15 +170,10 @@ func auditPullRequestSourceCode(repoConfig *utils.Repository, scanDetails *utils
 	}
 	// Set JAS output flags based on the scan results
 	repoConfig.OutputWriter.SetJasOutputFlags(scanResults.EntitledForJas, scanResults.HasJasScansResults(jasutils.Applicability))
-	workingDirs := []string{strings.TrimPrefix(sourceBranchWd, string(filepath.Separator))}
-	if targetBranchWd != "" && scanDetails.ResultsToCompare != nil {
-		log.Debug("Diff scan - converting to new issues...")
-		workingDirs = append(workingDirs, strings.TrimPrefix(targetBranchWd, string(filepath.Separator)))
-	}
-
 	filterFailedResultsIfScannersFailuresAreAllowed(scanDetails.ResultsToCompare, scanResults, repoConfig.Params.ConfigProfile.GeneralConfig.FailUponAnyScannerError, sourceBranchWd, targetBranchWd)
 
-	issuesCollection, e := scanResultsToIssuesCollection(scanResults, workingDirs...)
+	log.Debug("Diff scan - converting to new issues...")
+	issuesCollection, e := scanResultsToIssuesCollection(scanResults, strings.TrimPrefix(sourceBranchWd, string(filepath.Separator)), strings.TrimPrefix(targetBranchWd, string(filepath.Separator)))
 	if e != nil {
 		err = errors.Join(err, fmt.Errorf("failed to get issues for pull request. Error: %s", e.Error()))
 	}