diff --git a/nltools/data/design_matrix.py b/nltools/data/design_matrix.py
index 036b2d46..a8b83404 100644
--- a/nltools/data/design_matrix.py
+++ b/nltools/data/design_matrix.py
@@ -782,6 +782,8 @@ def clean(self, fill_na=0, exclude_polys=False, thresh=0.95, verbose=True):
             )
 
         old_settings = np.seterr(all="ignore")
+
+        out = self.copy()
         if fill_na is not None:
             out = self.fillna(fill_na)
 
diff --git a/nltools/tests/test_design_matrix.py b/nltools/tests/test_design_matrix.py
index 5c65dcb9..e6adbb17 100644
--- a/nltools/tests/test_design_matrix.py
+++ b/nltools/tests/test_design_matrix.py
@@ -138,6 +138,10 @@ def test_clean(sim_design_matrix):
     out = corr_cols.clean(verbose=True)
     assert out.shape[1] < corr_cols.shape[1]
 
+    # Test for bug #413 about args combinations
+    out = corr_cols.clean(fill_na=None, exclude_polys=True, verbose=True)
+    assert out.shape[1] < corr_cols.shape[1]
+
     # Raise an error if try to clean with an input matrix that has duplicate column names
     dup_cols = pd.concat([sim_design_matrix, sim_design_matrix], axis=1)
     with pytest.raises(ValueError):