One of the most annoying problems with the auto-brightness settings on iOS is that it sometimes doesn't adjust properly. Tech blog Addictive Tips shows how to fix this with a simple recalibration.
The way auto-brightness works in iOS 6 made improvements on previous iterations, but the downside is that it's now easy to break it if it's not set properly in the first place. For example, my iPad seemed to crank up the brightness every time I was in a dark room. That's the opposite of what I wanted.
To fix it, you need to head into the brightness settings (Settings > Brightness & Wallpaper), toggle auto-brightness off, and then adjust the brightness slider to the minimum setting when you're in a dark room. Next, toggle the auto-brightness setting back to "on", and it should be calibrated and working properly.
If that doesn't work, you can try calibrating both the maximum and minimum levels. This seemed to help me, so if you're having trouble with auto-brightness, it's worth a shot.
Fix iOS 6 Auto-Brightness Issues By Calibrating iPhone Light Sensors [Addictive Tips]