diff --git a/flake8_nitpick/__init__.py b/flake8_nitpick/__init__.py
index 9685d78b..414e0da5 100644
--- a/flake8_nitpick/__init__.py
+++ b/flake8_nitpick/__init__.py
@@ -293,7 +293,7 @@ def check_rules(self):
             yield self.file_error(105, f"Missing sections:\n{output}")
 
         generators = []
-        for section in expected_sections:
+        for section in expected_sections - missing_sections:
             expected_dict = self.file_toml[section]
             actual_dict = dict(setup_cfg[section])
             for diff_type, key, values in dictdiffer.diff(expected_dict, actual_dict):