The problem is the way you use it in fact.
As LabelEncoder is associating nominal feature to a numeric increment you should fit once and transform once the object has fitted. Don't forget that you need to have all your nominal feature in the training phase.
The good way to use it may be to have you nominal feature, do a fit on it, then only use the transform method.
>>> from sklearn import preprocessing
>>> le = preprocessing.LabelEncoder()
>>> le.fit([1, 2, 2, 6])
LabelEncoder()
>>> le.classes_
array([1, 2, 6])
>>> le.transform([1, 1, 2, 6])
array([0, 0, 1, 2]...)
from official doc
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