I have 2005 MCS 6spd with Auto Climate Control. Sometimes the air temperature will come out of the vents much hotter than expected, i.e, 72 degree F setting air feels like 80 - 85 degrees F. Wondering if this is the thermostat or something.

 

What's the external temperature and what's the internal?

It could be the internal thermostat isn't working, or blocked, there's one on the front panel somewhere.

Overall, I found the 05 was the worst MINI we had at maintaining a good temperatures. All our others have done a much better job. My problem was it blowing cold air on a sunny day, like it was listening to the sun sensor too much.

 

The inside temperature could be 70-72. Set the auto temp to 68 and warm air blows out. After a couple of minutes it may then start blowing cold. This is also independent of outside temperature. I would be interested to know where the internal thermostat is in the front panel.

 

If the auto button is pushed...the little green lite is lit....the computer will send extra warm/cool air to adjust the cabin temp based upon the cars temp and amount of light....ever notice how the fan does not blow fast till the car is warmed up..it is waiting for heat...
If the green lite is not lit...the air coming out the vents SHOULD roughly match the temp indicated....
I run mine in manual mode 90%+ of the time....

 

Have you looked in the manual, it shows it on the diagram. Here's the page, the temperature sensor is mark as 5.