Hi Gian,
This is on your Macmini6,2 with our not-entirely-official engineering fix for the ESXi+Macmini6,2 SMC problem, right? Or are you using one of the *ahem* other workarounds for running your Mac OS guest on that host hardware?
What's the exact error message you're getting through each of the two update methods (automatic and manual)? From which exact URL did you fetch the 10.8.2 manual updater?
I haven't had any problems installing the 10.8.2 combo update in a VM automatically and manually, and although I'm not 100% sure I have updated from 10.8.1 to 10.8.2, I think I did at some point... There's a chance it may have always been a direct installation of 10.8.2 onto 10.8.0.
It might be worth trying to download OS X Mountain Lion Update v10.8.1 and see if you can (re-)install 10.8.1 to clear up the problem.
Cheers,
--
Darius