Have had my 2015 2 door Hardtop JCW for less than a year and love it. But I opened the trunk and it was full of water, I had to open the drain plug and drain it. Carpet is saturated in trunk only. I have not opened the hatch in the rain. All the seals around the hatch are in tack and look to be in good condition. I cannot figure it out.
Does anyone think this will be covered under warranty? It has 5 months left on factory warranty plus it has a 2 year extended warranty from MINI. But I'm more concerned where the leak is coming from. Anyone else have this issue?

 

Several people have posted about these leaks, I'd do a search for it. Warranty would certainly cover it, bring it in for service.

 

Happened to me, it's the rear hatch seal. The dealer will replace it for free, it's a known issue.