There is a technical service bulletin on this issue. Here is the TSB. Take a look through it and let me know if it helps.
2008 Mini Cooper (R56) L4-1.6L (N12)
Body - Tailgate Will Not Latch Closed
Vehicle Body and Frame Technical Service Bulletins By Symptom Body - Tailgate Will Not Latch Closed
BODY - TAILGATE WILL NOT LATCH CLOSED
SI M51 07 08
This Service Information bulletin supersedes SI M51 07 08 dated May 2008.
[NEW] designates changes to this revision
Tailgate will not Latch Closed
R56 (Cooper and Cooper S) produced up to 4/2008
The tailgate latch will not latch in the closed position and the latch appears to be inoperative.
During assembly, the emergency release lever may have been pulled too hard. As a result, the black plastic ball which secures the cable to the latch may have broken off and become lodged in the latch.
A process improvement has taken place to prevent this situation.
1. Remove the rear latch cover trim per repair instruction RA 51 46 050.
2. [NEW] Early production cars have a manual release tether located under the rear seat bottom cushion, which has been eliminated from later production cars.
A. If the car does not have the manual release Bowden cable, operate the manual release lever of the latch, and then remove any debris which may be lodged in the latch.
B. If the car does have the manual release Bowden cable, determine whether it is still connected to the release lever on the latch. If the cable is NOT connected to the latch, the retaining lug is likely lodged in the latch. Continue with the following procedure.
3. Remove the lodged black plastic ball from the area around the release lever (1).
4. [NEW] Replace the emergency release Bowden cable per repair instruction RA 51 24 065.
If the vehicle was not equipped with a release cable from production, it should not be retrofitted to that car.
5. Ensure proper operation and reassemble the vehicle.
Covered under the terms of the MINI New Vehicle Limited Warranty.
Let me know if this helps or if you have questions.
Images (Click to enlarge)
Monday, March 16th, 2020 AT 1:09 PM