diff --git a/litellm/proxy/_experimental/mcp_server/discoverable_endpoints.py b/litellm/proxy/_experimental/mcp_server/discoverable_endpoints.py
index 0e2a4c257e7..3385e7feef6 100644
--- a/litellm/proxy/_experimental/mcp_server/discoverable_endpoints.py
+++ b/litellm/proxy/_experimental/mcp_server/discoverable_endpoints.py
@@ -691,8 +691,11 @@ async def openid_configuration(request: Request):
         if signer is not None:
             request_base_url = get_request_base_url(request)
             if isinstance(response, dict):
-                response["jwks_uri"] = f"{request_base_url}/.well-known/jwks.json"
-                response["id_token_signing_alg_values_supported"] = ["RS256"]
+                response = {
+                    **response,
+                    "jwks_uri": f"{request_base_url}/.well-known/jwks.json",
+                    "id_token_signing_alg_values_supported": ["RS256"],
+                }
     except ImportError:
         pass
 
diff --git a/litellm/proxy/_experimental/mcp_server/mcp_server_manager.py b/litellm/proxy/_experimental/mcp_server/mcp_server_manager.py
index 0208f52968d..c66dc307089 100644
--- a/litellm/proxy/_experimental/mcp_server/mcp_server_manager.py
+++ b/litellm/proxy/_experimental/mcp_server/mcp_server_manager.py
@@ -2135,6 +2135,12 @@ class MCPServerManager:
         if hook_extra_headers:
             if extra_headers is None:
                 extra_headers = {}
+            if "Authorization" in extra_headers and "Authorization" in hook_extra_headers:
+                verbose_logger.warning(
+                    "MCPServerManager: hook_extra_headers contains 'Authorization' which will "
+                    "overwrite the existing Authorization header set by static_headers or server "
+                    "authentication. The hook JWT will take precedence."
+                )
             extra_headers.update(hook_extra_headers)
 
         stdio_env = self._build_stdio_env(mcp_server, raw_headers)
diff --git a/litellm/proxy/guardrails/guardrail_hooks/mcp_jwt_signer/__init__.py b/litellm/proxy/guardrails/guardrail_hooks/mcp_jwt_signer/__init__.py
index d4a6c579097..230edaec855 100644
--- a/litellm/proxy/guardrails/guardrail_hooks/mcp_jwt_signer/__init__.py
+++ b/litellm/proxy/guardrails/guardrail_hooks/mcp_jwt_signer/__init__.py
@@ -4,7 +4,7 @@ from typing import TYPE_CHECKING
 
 from litellm.types.guardrails import SupportedGuardrailIntegrations
 
-from .mcp_jwt_signer import MCPJWTSigner, _mcp_jwt_signer_instance, get_mcp_jwt_signer
+from .mcp_jwt_signer import MCPJWTSigner, get_mcp_jwt_signer
 
 if TYPE_CHECKING:
     from litellm.types.guardrails import Guardrail, LitellmParams
@@ -51,6 +51,5 @@ guardrail_class_registry = {
 __all__ = [
     "MCPJWTSigner",
     "initialize_guardrail",
-    "_mcp_jwt_signer_instance",
     "get_mcp_jwt_signer",
 ]
diff --git a/litellm/proxy/guardrails/guardrail_hooks/mcp_jwt_signer/mcp_jwt_signer.py b/litellm/proxy/guardrails/guardrail_hooks/mcp_jwt_signer/mcp_jwt_signer.py
index 12a06da2897..4fe51ba2fbc 100644
--- a/litellm/proxy/guardrails/guardrail_hooks/mcp_jwt_signer/mcp_jwt_signer.py
+++ b/litellm/proxy/guardrails/guardrail_hooks/mcp_jwt_signer/mcp_jwt_signer.py
@@ -27,6 +27,7 @@ your own RSA keypair. If unset, an RSA-2048 keypair is auto-generated at startup
 import base64
 import hashlib
 import os
+import re
 import time
 from typing import Any, Dict, Optional, Union
 
@@ -169,6 +170,12 @@ class MCPJWTSigner(CustomGuardrail):
 
         # Register singleton so the JWKS endpoint can access it.
         global _mcp_jwt_signer_instance
+        if _mcp_jwt_signer_instance is not None:
+            verbose_proxy_logger.warning(
+                "MCPJWTSigner: replacing existing singleton — previously issued tokens "
+                "signed with the old key will fail JWKS verification. "
+                "Avoid configuring multiple mcp_jwt_signer guardrails."
+            )
         _mcp_jwt_signer_instance = self
 
         verbose_proxy_logger.info(
@@ -265,11 +272,19 @@ class MCPJWTSigner(CustomGuardrail):
         if end_user_id:
             claims["end_user_id"] = end_user_id
 
-        # scope: tool-level access
-        tool_name: str = data.get("mcp_tool_name", "")
-        scopes = ["mcp:tools/call", "mcp:tools/list"]
+        # scope: minimal tool-level access.
+        # Only grant mcp:tools/list when no specific tool is being called —
+        # tool call JWTs should not carry enumeration permissions.
+        # Tool names are sanitized (alphanumeric + _ and -) before embedding
+        # so path-traversal or malformed scope values cannot be injected.
+        import re
+
+        raw_tool_name: str = data.get("mcp_tool_name", "")
+        tool_name = re.sub(r"[^a-zA-Z0-9_\-]", "_", raw_tool_name) if raw_tool_name else ""
         if tool_name:
-            scopes.append(f"mcp:tools/{tool_name}:call")
+            scopes = ["mcp:tools/call", f"mcp:tools/{tool_name}:call"]
+        else:
+            scopes = ["mcp:tools/call", "mcp:tools/list"]
         claims["scope"] = " ".join(scopes)
 
         return claims
@@ -301,9 +316,11 @@ class MCPJWTSigner(CustomGuardrail):
             algorithm=self.ALGORITHM,
         )
 
-        data["extra_headers"] = {
-            "Authorization": f"Bearer {signed_token}",
-        }
+        # Merge into existing extra_headers rather than replacing — a prior guardrail
+        # in the chain may have already injected headers (e.g. tracing, correlation IDs).
+        # MCPJWTSigner sets Authorization last so its JWT takes precedence.
+        existing_headers: Dict[str, str] = data.get("extra_headers") or {}
+        data["extra_headers"] = {**existing_headers, "Authorization": f"Bearer {signed_token}"}
 
         verbose_proxy_logger.debug(
             "MCPJWTSigner: signed JWT sub=%s act=%s tool=%s exp=%d",
diff --git a/tests/test_litellm/proxy/_experimental/mcp_server/test_mcp_hook_extra_headers.py b/tests/test_litellm/proxy/_experimental/mcp_server/test_mcp_hook_extra_headers.py
index 40242f70e38..32f3a340855 100644
--- a/tests/test_litellm/proxy/_experimental/mcp_server/test_mcp_hook_extra_headers.py
+++ b/tests/test_litellm/proxy/_experimental/mcp_server/test_mcp_hook_extra_headers.py
@@ -6,7 +6,7 @@ Validates that:
 2. pre_call_tool_check returns hook-provided extra_headers AND modified arguments
 3. call_tool flows hook headers and modified arguments downstream
 4. Hook-provided headers take highest priority (merge after static_headers)
-5. OpenAPI-backed servers raise HTTPException when hook headers are present
+5. OpenAPI-backed servers log a warning and continue (skip injection) when hook headers are present
 6. JWT claims are propagated in both standard and virtual-key fast paths
 7. Backward compatibility: hooks without extra_headers continue to work
 """
diff --git a/tests/test_litellm/proxy/guardrails/test_mcp_jwt_signer.py b/tests/test_litellm/proxy/guardrails/test_mcp_jwt_signer.py
index bc0b398cd84..991f813c675 100644
--- a/tests/test_litellm/proxy/guardrails/test_mcp_jwt_signer.py
+++ b/tests/test_litellm/proxy/guardrails/test_mcp_jwt_signer.py
@@ -201,12 +201,13 @@ def test_build_claims_scope_with_tool():
 
     scopes = set(claims["scope"].split())
     assert "mcp:tools/call" in scopes
-    assert "mcp:tools/list" in scopes
     assert "mcp:tools/search_web:call" in scopes
+    # Tool-call JWTs must NOT carry mcp:tools/list — least-privilege
+    assert "mcp:tools/list" not in scopes
 
 
 def test_build_claims_scope_without_tool():
-    """_build_claims() omits per-tool scope when mcp_tool_name is not set."""
+    """_build_claims() includes mcp:tools/list when no specific tool is called."""
     signer = _make_signer()
     user_dict = _make_user_api_key_dict()
     data: Dict[str, Any] = {}
@@ -216,9 +217,8 @@ def test_build_claims_scope_without_tool():
     scopes = set(claims["scope"].split())
     assert "mcp:tools/call" in scopes
     assert "mcp:tools/list" in scopes
-    # No per-tool scope
-    for scope in scopes:
-        assert ":" not in scope.replace("mcp:", "") or scope.endswith(":call") is False or scope == "mcp:tools/call"
+    # No per-tool call scope when no tool name was given
+    assert not any(s.endswith(":call") and s != "mcp:tools/call" for s in scopes)
 
 
 def test_build_claims_act_fallback_to_litellm_proxy():