diff --git a/hermes_cli/skills_hub.py b/hermes_cli/skills_hub.py
index 54adef6fdf..9e0286d85f 100644
--- a/hermes_cli/skills_hub.py
+++ b/hermes_cli/skills_hub.py
@@ -341,7 +341,13 @@ def do_search(query: str, source: str = "all", limit: int = 10, console: Optiona
     c.print(table)
     c.print("[dim]Use: hermes skills inspect <identifier> to preview, "
             "hermes skills install <identifier> to install "
-            "(--json for scripting)[/]\n")
+            "(--json for scripting)[/]")
+    if any(r.source in ("skills.sh", "skills-sh") for r in results):
+        c.print("[dim yellow]Note:[/] [dim]skills.sh results may include entries whose "
+                "upstream files were removed or renamed; a 'stale index entry' error "
+                "at install means the skill no longer exists there.[/]\n")
+    else:
+        c.print()
 
 
 def _rank_and_page(all_results, page: int, page_size: int):
@@ -585,7 +591,16 @@ def _pinned_sources(c: Console, sources, source_id: Optional[str], identifier: s
     return None
 
 
-def _print_fetch_failure(c: Console, sources, identifier: str) -> None:
+def _print_fetch_failure(c: Console, sources, identifier: str, meta=None, source=None) -> None:
+    # Index hit but files gone (GitHub 404): a stale index entry, not a user
+    # typo — name it so users stop re-trying spellings (#3259).
+    if meta is not None:
+        src_id = getattr(source, "source_id", lambda: "the registry")()
+        c.print(f"[bold red]Error:[/] '{identifier}' is listed in the {src_id} index, "
+                f"but its files no longer exist upstream.")
+        c.print("[dim]Stale index entry: the skill was likely renamed or removed by "
+                "its author. Try `hermes skills search` for an alternative.[/]\n")
+        return
     rate_limited = any(getattr(src, "is_rate_limited", False)
                        or getattr(getattr(src, "github", None), "is_rate_limited", False)
                        for src in sources)
@@ -663,7 +678,7 @@ def do_install(identifier: str, category: str = "", force: bool = False,
     c.print(f"\n[bold]Fetching:[/] {identifier}")
     meta, bundle, _matched_source = _resolve_source_meta_and_bundle(identifier, sources)
     if not bundle:
-        _print_fetch_failure(c, sources, identifier)
+        _print_fetch_failure(c, sources, identifier, meta=meta, source=_matched_source)
         return
     if not _resolve_url_bundle_name(c, bundle, meta, identifier, name_override, skip_confirm):
         return
diff --git a/tests/hermes_cli/test_skills_hub.py b/tests/hermes_cli/test_skills_hub.py
index b7f7cc2802..444dd38e98 100644
--- a/tests/hermes_cli/test_skills_hub.py
+++ b/tests/hermes_cli/test_skills_hub.py
@@ -496,3 +496,81 @@ def test_do_update_unmodified_skill_updates_normally(monkeypatch, tmp_path):
 
     assert installs == ["someone/hub-skill"]
     assert "Updated 1 skill(s)" in sink.getvalue()
+
+
+# ---------------------------------------------------------------------------
+# Stale index entry messages (#3259)
+# ---------------------------------------------------------------------------
+
+
+def _stale_env(monkeypatch):
+    """do_install where the index has metadata but the files are gone (404)."""
+    import hermes_cli.skills_hub as cli_hub
+    import tools.skills_hub as hub
+
+    class StaleSource:
+        def source_id(self):
+            return "skills-sh"
+
+    meta = type("Meta", (), {"identifier": "skills-sh/org/gone-skill"})()
+    monkeypatch.setattr(hub, "ensure_hub_dirs", lambda: None)
+    monkeypatch.setattr(cli_hub, "_sources", lambda: [StaleSource()])
+    monkeypatch.setattr(
+        cli_hub, "_resolve_source_meta_and_bundle",
+        lambda identifier, sources: (meta, None, sources[0]))
+    sink = StringIO()
+    console = Console(file=sink, force_terminal=False, color_system=None)
+    return console, sink
+
+
+def test_do_install_stale_index_names_the_problem(monkeypatch):
+    """Index hit + missing files reads as a stale entry, not a typo (#3259)."""
+    from hermes_cli.skills_hub import do_install
+
+    console, sink = _stale_env(monkeypatch)
+    do_install("skills-sh/org/gone-skill", console=console, skip_confirm=True)
+
+    out = sink.getvalue()
+    assert "Stale index entry" in out
+    assert "skills-sh" in out
+    assert "Could not fetch" not in out
+
+
+def test_do_install_unknown_identifier_stays_generic(monkeypatch):
+    """No index hit at all keeps the original generic message."""
+    import hermes_cli.skills_hub as cli_hub
+    import tools.skills_hub as hub
+    from hermes_cli.skills_hub import do_install
+
+    monkeypatch.setattr(hub, "ensure_hub_dirs", lambda: None)
+    monkeypatch.setattr(cli_hub, "_sources", lambda: [object()])
+    monkeypatch.setattr(
+        cli_hub, "_resolve_source_meta_and_bundle",
+        lambda identifier, sources: (None, None, None))
+    sink = StringIO()
+    console = Console(file=sink, force_terminal=False, color_system=None)
+    do_install("nobody/nowhere/nothing", console=console, skip_confirm=True)
+
+    out = sink.getvalue()
+    assert "Could not fetch" in out
+    assert "Stale index entry" not in out
+
+
+def test_do_search_warns_about_skills_sh_staleness(monkeypatch):
+    """Search results from skills.sh carry the stale-index caveat."""
+    import tools.skills_hub_search as hub_search
+    from hermes_cli.skills_hub import do_search
+    import hermes_cli.skills_hub as cli_hub
+
+    row = type("Row", (), {
+        "name": "gone-skill", "description": "d", "source": "skills-sh",
+        "trust_level": "community",
+        "identifier": "skills-sh/org/gone-skill"})()
+    monkeypatch.setattr(cli_hub, "_sources", lambda: [])
+    monkeypatch.setattr(hub_search, "unified_search",
+                        lambda query, sources, source_filter, limit: [row])
+    sink = StringIO()
+    console = Console(file=sink, force_terminal=False, color_system=None)
+    do_search("gone", console=console)
+
+    assert "stale index entry" in sink.getvalue()