diff --git a/cmd.go b/cmd.go
index c11367f..6955a94 100644
--- a/cmd.go
+++ b/cmd.go
@@ -178,9 +178,27 @@ func testCmd() *cobra.Command {
 				}
 
 				if update && len(fileOwnResults) > 0 {
-					updated := rewriteFile(parsed, fileOwnResults, string(content))
-					if updated != string(content) {
-						_ = os.WriteFile(filePath, []byte(updated), 0o644)
+					// Refuse to write if actual output contains "$ " lines —
+					// they'd be misparsed as commands on the next read.
+					hasConflict := false
+					for _, r := range fileOwnResults {
+						for _, line := range r.Actual {
+							if strings.HasPrefix(line, "$ ") {
+								hasConflict = true
+								break
+							}
+						}
+						if hasConflict {
+							break
+						}
+					}
+					if hasConflict {
+						fmt.Fprintf(os.Stderr, "warning: %s: skipping --update because output contains lines starting with '$ '\n", parsed.Path)
+					} else {
+						updated := rewriteFile(parsed, fileOwnResults, string(content))
+						if updated != string(content) {
+							_ = os.WriteFile(filePath, []byte(updated), 0o644)
+						}
 					}
 				}
 
diff --git a/run.go b/run.go
index 3aace4b..bf01c17 100644
--- a/run.go
+++ b/run.go
@@ -162,8 +162,9 @@ func runFile(file ShoutFile, opts RunOptions) FileResult {
 		return FileResult{File: file, TmpDir: tmpDir, Error: err.Error()}
 	}
 
+	var waited bool
 	defer func() {
-		if cmd.Process != nil {
+		if !waited && cmd.Process != nil {
 			_ = syscall.Kill(-cmd.Process.Pid, syscall.SIGKILL)
 		}
 	}()
@@ -188,6 +189,11 @@ func runFile(file ShoutFile, opts RunOptions) FileResult {
 	select {
 	case r := <-ch:
 		if r.err != nil {
+			if cmd.Process != nil {
+				_ = syscall.Kill(-cmd.Process.Pid, syscall.SIGKILL)
+			}
+			_ = cmd.Wait()
+			waited = true
 			return FileResult{File: file, TmpDir: tmpDir, Error: r.err.Error()}
 		}
 		output = r.data
@@ -197,10 +203,12 @@ func runFile(file ShoutFile, opts RunOptions) FileResult {
 		}
 		<-ch // drain the reader goroutine so pipe FDs are released
 		_ = cmd.Wait()
+		waited = true
 		return FileResult{File: file, TmpDir: tmpDir, Error: "Timeout reading output"}
 	}
 
 	_ = cmd.Wait()
+	waited = true
 
 	outputs, exitCodesList := parseSentinelOutput(string(output), len(file.Commands), sentinel)
 
diff --git a/shout b/shout
index 35d7112..8aa9845 100755
Binary files a/shout and b/shout differ
diff --git a/update.go b/update.go
index 5628aee..b71894f 100644
--- a/update.go
+++ b/update.go
@@ -79,8 +79,6 @@ func rewriteFile(file ShoutFile, results []CommandResult, originalContent string
 				marker := updateExitCodeMarker(cmd, result.ExitCode)
 				if marker != "" {
 					output = append(output, marker)
-				} else if len(content) > 0 && exitCodeMarkerRe.MatchString(content[len(content)-1]) {
-					output = append(output, "[0]")
 				}
 				for k := 0; k < rawTrailing; k++ {
 					output = append(output, "")