diff --git a/cmd/scatr/version.go b/cmd/scatr/version.go
index 4d36d80..0229955 100644
--- a/cmd/scatr/version.go
+++ b/cmd/scatr/version.go
@@ -7,7 +7,7 @@ import (
 	"github.com/spf13/cobra"
 )
 
-const version = "0.4.0"
+const version = "0.4.1"
 
 var versionCmd = &cobra.Command{
 	Use:   "version",
diff --git a/runner/diff.go b/runner/diff.go
index bab69d2..ccd6934 100644
--- a/runner/diff.go
+++ b/runner/diff.go
@@ -37,6 +37,12 @@ func matchFileNameIssueCodes(files map[string]*pragma.File, analysisResult *Resu
 	}
 
 	for _, file := range files {
+		// If the file already has an ignore/check pragma, that takes priority.
+		// Don't check its file name in that case.
+		if file.CheckMode != pragma.CheckAll {
+			continue
+		}
+
 		_, exists := analysisIssueCodes[file.Name]
 		if !exists {
 			continue