diff --git a/lib/context-bill.ts b/lib/context-bill.ts
index 0cd882868..342b95e39 100644
--- a/lib/context-bill.ts
+++ b/lib/context-bill.ts
@@ -210,6 +210,14 @@ function parseFrontmatter(text: string): { bytes: number; keys: string[]; block:
  * Dirent type check sees none of them. Dangling links and anything that is
  * neither a file nor a directory are null.
  */
+function isFile(p: string): boolean {
+  try {
+    return fs.statSync(p).isFile();
+  } catch {
+    return false;
+  }
+}
+
 function entryKind(p: string, e: fs.Dirent): "file" | "dir" | null {
   if (e.isFile()) return "file";
   if (e.isDirectory()) return "dir";
@@ -289,7 +297,7 @@ export function walkMd(dir: string, opts: { billedRoot?: string; skipNestedSkill
       } else if (
         kind !== "dir" ||
         fs.existsSync(path.join(p, ".git")) ||
-        (opts.skipNestedSkills && current === dir && fs.existsSync(path.join(p, "SKILL.md")))
+        (opts.skipNestedSkills && current === dir && isFile(path.join(p, "SKILL.md")))
       ) {
         continue;
       }
diff --git a/test/context-bill.test.ts b/test/context-bill.test.ts
index 024e4cd06..304d0efae 100644
--- a/test/context-bill.test.ts
+++ b/test/context-bill.test.ts
@@ -391,6 +391,17 @@ describe("upstream fix b: installed-tree layout (repo-checkout subdir skip)", ()
     fs.rmSync(root, { recursive: true, force: true });
   });
 
+  it("bills a subdirectory whose SKILL.md is a directory to its container, as discovery does not count it as a skill", () => {
+    const root = fs.mkdtempSync(path.join(os.tmpdir(), "context-bill-skilldir-"));
+    fs.writeFileSync(path.join(root, "SKILL.md"), "---\nname: c\ndescription: d\n---\n# c\n");
+    fs.mkdirSync(path.join(root, "sub", "SKILL.md"), { recursive: true });
+    fs.writeFileSync(path.join(root, "sub", "notes.md"), "n".repeat(500));
+    const bill = buildBill(root);
+    fs.rmSync(root, { recursive: true, force: true });
+    expect(bill.skills.map((s) => s.name)).toEqual([path.basename(root)]);
+    expect(bill.skills[0].totalMdBytes).toBe(bill.skills[0].skillMdBytes + 500);
+  });
+
   it("refuses a parent link when the root's own name starts with '..'", () => {
     if (process.platform === "win32") return;
     const tmp = fs.mkdtempSync(path.join(os.tmpdir(), "context-bill-dotdot-"));