Just to clarify, you will commonly get an element of discolouration, as well as the rainbow colouring from the weld heat and light rusting under the clear powder on a naked frame. You should NOT get large areas, areas which are raised and so on.
Think of the trend around at the moment where people buy up older vehicles and lacquer over them to keep them in the condition they were found - the Naked is picking up on this trend, albeit with ultra modern brakes and suspension, carbon fibre and a 'Naked' frame - where you see everything. If you don't like to see everything on the frame then the Naked probably isn't the right bike for you - get a black framed Blackline or Polished line Dominator and spec an aluminium tank as an option.
If you have a bike you are concerned about and it is within it's warranty (12 months on paint and trim), then report your concerns to your local dealer.
Obviously we can not account for environmental damage such as stone chips and improper maintenance.