I have noticed that there is water / condensation in the boot well where the spare wheel is kept, the carpet is dry in the boot and can't see any leaks around the seals or rear wiper motor

Any idea why?

It can happen for no reason other than a humid interior, insufficient ventilation and cold weather chilling the uninsulated metal where condensation forms.

Is your rear washer working?

 

If not then that might give you a clue!

Yes rear washer working, boot is not wet, carpet bone dry, just wheel well area is causing the spate wheel to rust 

Check the security of the bungs, dry area then apply WD-40.