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This is common on the mini's. I have this as well and will have the dealer fix this when I take the car in for service. I suggest you take it to the dealer for them to make adjustments.
Until you can get to the dealer, put a couple wraps of electrical tape around the "D" shaped latch on the hatch. That will eliminate the noise, and lasts 6+ months before needing some new tape. Man, that was annoying until I figured out where it was coming from.
I just did mine right after work (12am) and I will drive the car around today to see if the tape did anything. I really hope it did as it sounds like the car wants to fall apart at times.
There is actually a factory fix for this. Mini will do a fix for this at no charge. I compalined about this when I was having some other service done, and there was a bulletin sent out to the dealerships. The replace the two screws that attach the rear bumper cover which is visible when you open the hatch, and then place rubber stoppers on them. Mine is quite as can be now.
Problem is sometimes it comes back even after the fix. I've had my latch and ring replaced twice and "adjusted" several times. Last fix lasted almost 9 months but rattle is back now.
I just did the tape mod on the latch bracket on the boot and that has fixed the problem! I will stick with this for awhile and see how long it last and put a new piece on there when I need to! I am happy to not have that annoying knocking coming from the back!