Old-school observation here -- the darker blue at the top is probably not a flaw, but part of the polarized band, which naturally occurs at about 90-degrees from the sun.
You can only capture this with a clear-blue sky and a very wide lens, both of which you have here.
It can be very difficult to see with the naked eye, but you can locate it easily; make an "L" with your thumb and index finger, point at the sum, and wherever your thumb can point, the sky will photograph bluer (and polarizing lenses will become more effective!)