diff --git a/mypy/stubtest.py b/mypy/stubtest.py
index 36cd0a213d4d..6c8d03319893 100644
--- a/mypy/stubtest.py
+++ b/mypy/stubtest.py
@@ -568,6 +568,13 @@ def verify_typeinfo(
             # Catch all exceptions in case the runtime raises an unexpected exception
             # from __getattr__ or similar.
             continue
+
+        # If it came from the metaclass, consider the runtime_attr to be MISSING
+        # for a more accurate message
+        if runtime_attr is not MISSING and type(runtime) is not runtime:
+            if getattr(runtime_attr, "__objclass__", None) is type(runtime):
+                runtime_attr = MISSING
+
         # Do not error for an object missing from the stub
         # If the runtime object is a types.WrapperDescriptorType object
         # and has a non-special dunder name.
@@ -1519,6 +1526,7 @@ def is_probably_a_function(runtime: Any) -> bool:
         isinstance(runtime, (types.FunctionType, types.BuiltinFunctionType))
         or isinstance(runtime, (types.MethodType, types.BuiltinMethodType))
         or (inspect.ismethoddescriptor(runtime) and callable(runtime))
+        or (isinstance(runtime, types.MethodWrapperType) and callable(runtime))
     )
 
 
diff --git a/mypy/test/teststubtest.py b/mypy/test/teststubtest.py
index fcbf07b4d371..b16cb18ace21 100644
--- a/mypy/test/teststubtest.py
+++ b/mypy/test/teststubtest.py
@@ -1460,6 +1460,16 @@ def h(x: str): ...
             runtime="__all__ += ['Z']\nclass Z:\n  def __reduce__(self): return (Z,)",
             error=None,
         )
+        # __call__ exists on type, so it appears to exist on the class.
+        # This checks that we identify it as missing at runtime anyway.
+        yield Case(
+            stub="""
+            class ClassWithMetaclassOverride:
+                def __call__(*args, **kwds): ...
+            """,
+            runtime="class ClassWithMetaclassOverride: ...",
+            error="ClassWithMetaclassOverride.__call__",
+        )
 
     @collect_cases
     def test_missing_no_runtime_all(self) -> Iterator[Case]: