Water getting in and puddling the spare wheel. I can tell you exactly where its getting in. My my other half bought a 55 plate Focus a couple of years ago, and seemed nice and clean with low miles for age. Opening the tailgate after a couple of days worth of rain, there must have been a gallon of water in the boot along with a drenched boot carpet. After much searching, taking out light clusters etc, all to no avail, I shoved my missus in the boot with a torch and went round the rear of the car with a fairy liquid bottle full of water and found it to be the welded seal near the tailgate hinge, following right behind the roof rail. Some clear bathroom sealer injected and smoothed off solved the problem for good. its a tiny gap that you wouldn't believe lets so much water in.