Things that the 1.2 firmware broke. Using either of the available upgrades, 1.1 or 1.2, seems to have the ability to break the manual focus settings on some cameras. My camera had this problem after the 1.1 upgrade, and still has it. If the manual focus settings are improtant to you, you might want to wait on upgrading until Nikon comes up with a solution. Read more on this page.
Exposure lock white balance problem.
If you take panorama shots with user white balances, then watch out for version 1.2. I'm not entirely sure if this is new with 1.2 or not, but I have never noticed it before. Switch the camera to M-Rec in a dark environment that will require a long exposure. This isn't really a bug, just unusual. I received another comment from someone who has seen this too.