I just finished changing the alternator in my 2013 R56. BTW I did not put it in service mode; instead pulled it out the top by lifting the right side of the engine.
Anyway, when I reconnected the battery neg. cable I see a tiny spark and hear a little click. That tells me something gets turned on and that tells me that the battery will draw down.
Can anyone tell me what's happening?

 

It's normal. Any dash warning lights? Engine running smoothly?

 

That spark was completing the circuit of the cars door window controls, key remote wifi and several other small electrical circuits that a mini cooper was engineered to do. It is normal and the battery will drain down after about 2-4 weeks of not starting the car. Again all normal.

 

Great, thanks to both of you. I've been monitoring the voltage with my meter and it seems to be holding.