diff --git a/pyglove/core/geno/base.py b/pyglove/core/geno/base.py
index 1a516fb..8e8e525 100644
--- a/pyglove/core/geno/base.py
+++ b/pyglove/core/geno/base.py
@@ -1348,7 +1348,7 @@ def from_fn(
               f'Choices: {dna_spec.num_choices}, '
               f'Location: {dna_spec.location.path}.')
         children = []
-        for i, choice in enumerate(decision):  # pyrefly: ignore[bad-argument-type]
+        for i, choice in enumerate(decision):  # pyrefly: ignore[bad-argument-type, not-iterable]
           choice_location = utils.KeyPath(i, dna_spec.location)
           if not isinstance(choice, int):
             raise ValueError(
diff --git a/pyglove/core/hyper/categorical.py b/pyglove/core/hyper/categorical.py
index b26e3cb..8084f48 100644
--- a/pyglove/core/hyper/categorical.py
+++ b/pyglove/core/hyper/categorical.py
@@ -192,7 +192,7 @@ def _decode(self) -> List[Any]:
               )
           )
       choices = []
-      for i, sub_dna in enumerate(dna):  # pyrefly: ignore[bad-argument-type]
+      for i, sub_dna in enumerate(dna):  # pyrefly: ignore[bad-argument-type, not-iterable]
         if not isinstance(sub_dna.value, int):
           raise ValueError(
               utils.message_on_path(
diff --git a/pyglove/core/symbolic/class_wrapper.py b/pyglove/core/symbolic/class_wrapper.py
index 07e3c27..4a76e4c 100644
--- a/pyglove/core/symbolic/class_wrapper.py
+++ b/pyglove/core/symbolic/class_wrapper.py
@@ -466,7 +466,7 @@ def wrap_module(
   origin_cls_to_wrap_cls = {}
   for symbol_name in (names or dir(module)):
     s = getattr(module, symbol_name)
-    if inspect.isclass(s) and (not where or where(s)):
+    if inspect.isclass(s) and (not where or where(s)):  # pyrefly: ignore[bad-argument-type]
       # NOTE(daiyip): It's possible that a name under a module is an alias for
       # another class. In such case, we do not create duplicated wrappers but
       # shares the same wrapper classes with different names.