Length mismatch error in ColumnTransformer sklearn v - pandas

Question

Length Mismatch error when setting transform_output to "pandas" on the custom transformer (deleting NaN values)
I'm implementing the custom transformer to delete the rows containing NaNs. The code is
from sklearn.base import BaseEstimator,TransformerMixin
class NaRemover(BaseEstimator,TransformerMixin):
def __init__(self):
self._columns = []
def fit(self, X):
self._columns = X.columns.values
return self
def transform(self, X):
X = X.dropna()
return X
It works correctly as standalone.
Then I put it in the ColumnTransformer:
features = X_train.columns.values
ct_nan = ColumnTransformer([('delete_na',NaRemover(),features)])
ct_nan.fit(X_train)
and get the error:
ValueError: Length mismatch: Expected axis has 109 elements, new values have 140 elements
Problem is caused by the function that wraps the output into the pandas dataframe
129 # dense_config == "pandas"
--> 130 return _wrap_in_pandas_container(
131 data_to_wrap=data_to_wrap,
132 index=getattr(original_input, "index", None),
As far as could gather, it checks the integrity of the dataframe index, which I obviously destroy when applying transform (although I don't understand why should it check it on the fit stage)
214 def set_axis(self, axis: int, new_labels: Index) -> None:
215 # Caller is responsible for ensuring we have an Index object.
--> 216 self._validate_set_axis(axis, new_labels)
217 self.axes[axis] = new_labels
218
/usr/local/lib/python3.8/dist-packages/pandas/core/internals/base.py in _validate_set_axis(self, axis, new_labels)
55
56 elif new_len != old_len:
---> 57 raise ValueError(
58 f"Length mismatch: Expected axis has {old_len} elements, new "
59 f"values have {new_len} elements"
Is it what the functionality supposed to be? Are the transformers changing the shape of the dataframe not allowed? And if not, how can I overcome the problem?