diff --git a/lib/clean/caches.sh b/lib/clean/caches.sh
index 72892ce..463996b 100644
--- a/lib/clean/caches.sh
+++ b/lib/clean/caches.sh
@@ -212,7 +212,9 @@ clean_project_caches() {
                 [[ -d "$cache_dir/cache" ]] && safe_clean "$cache_dir/cache"/* "Next.js build cache" || true
                 ;;
             "__pycache__")
-                [[ -d "$cache_dir" ]] && safe_clean "$cache_dir"/* "Python bytecode cache" || true
+                # Remove the cache directory itself so we avoid expanding every
+                # .pyc file into a separate safe_clean target.
+                [[ -d "$cache_dir" ]] && safe_clean "$cache_dir" "Python bytecode cache" || true
                 ;;
             ".dart_tool")
                 if [[ -d "$cache_dir" ]]; then
diff --git a/tests/clean_system_caches.bats b/tests/clean_system_caches.bats
index 0275c70..bfd2930 100644
--- a/tests/clean_system_caches.bats
+++ b/tests/clean_system_caches.bats
@@ -138,6 +138,25 @@ setup() {
     rm -rf "$HOME/Projects"
 }
 
+@test "clean_project_caches removes pycache directories as single targets" {
+    mkdir -p "$HOME/Projects/python-app/__pycache__"
+    touch "$HOME/Projects/python-app/pyproject.toml"
+    touch "$HOME/Projects/python-app/__pycache__/module.pyc"
+
+    run env HOME="$HOME" PROJECT_ROOT="$PROJECT_ROOT" bash --noprofile --norc <<'EOF'
+set -euo pipefail
+source "$PROJECT_ROOT/lib/core/common.sh"
+source "$PROJECT_ROOT/lib/clean/caches.sh"
+safe_clean() { echo "$2|$1"; }
+clean_project_caches
+EOF
+    [ "$status" -eq 0 ]
+    [[ "$output" == *"Python bytecode cache|$HOME/Projects/python-app/__pycache__"* ]]
+    [[ "$output" != *"module.pyc"* ]]
+
+    rm -rf "$HOME/Projects"
+}
+
 @test "clean_project_caches scans configured roots instead of HOME" {
     mkdir -p "$HOME/.config/mole"
     mkdir -p "$HOME/CustomProjects/app/.next/cache"