There are two issues. Firstly, you're not transposing the multiplier. Secondly, you're using elementwise multiplication instead of matrix multiplication.
Here is how you can fix both issues:
In [18]: np.linalg.eig(np.matmul(H, H.T))
Out[18]:
(array([1.94501343e+00, 1.14315435e-05, 4.49751401e-02]),
array([[-0.35979589, -0.82953709, 0.42710084],
[-0.81600749, 0.05780546, -0.57514373],
[-0.4524143 , 0.55545183, 0.69770664]]))
Alternatively, you could use np.matrix to make the * perform matrix multiplication:
In [22]: H = np.matrix([[0.1, 0.3, .4],[0.5 , 0.5, 0.9],[0.1, 0.4, 0.5]])
In [23]: np.linalg.eig(H*H.T)
Out[23]:
(array([1.94501343e+00, 1.14315435e-05, 4.49751401e-02]),
matrix([[-0.35979589, -0.82953709, 0.42710084],
[-0.81600749, 0.05780546, -0.57514373],
[-0.4524143 , 0.55545183, 0.69770664]]))
If the matrix contains complex numbers you should be using conjugate transpose (.H) instead of transpose (.T). I've chosen to not do this to avoid confusing notation (H*H.H).