numpy array: IndexError: too many indices for array

Numpy ndarrays are meant for all elements to have the same length. In this case, your second array doesn’t contain lists of the same length, so it ends up being a 1-D array of lists, as opposed to a “proper” 2-D array.

From the Numpy docs on N-dimensional arrays:

An ndarray is a (usually fixed-size) multidimensional container of items of the same type and size.

a = np.array([[1,2,3,4], [5,6,7,8], [9,10,11,12]])
a.shape # (3,4)
a.ndim # 2

b = np.array([[1,2,3,4], [5,6,7,8], [9,10,11]])
b.shape # (3,)
b.ndim # 1

This discussion may be useful.