Update scripts/bash/setup-plan.sh

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: Ray0907

scripts/bash/setup-plan.sh

@@ -34,7 +34,11 @@ eval $(get_feature_paths)
 check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 
 # Check if branch and spec directory are in sync
-check_and_fix_spec_directory_mismatch || exit 1
+check_and_fix_spec_directory_mismatch
+result=$?
+if [[ $result -ne 0 && $result -ne 1 ]]; then
+    exit 1
+fi
 
 # Ensure the feature directory exists
 mkdir -p "$FEATURE_DIR"