Matrix metering isn't good when its voodoo guesses wrong - back-lighting is a classic, though with D-lenses (that tell it where they're focused) it can do some magic.  Lots of light or dark areas in the frame can confuse it too. Snow, sand, etc.

One recent example that occurs to me is shooting a small stained glass window from inside the church.

The camera decided it was really dark because the window only took up a relatvely small amount of the frame, while I really wanted to expose for the light outside the window, which made the interior stone black but showed the colours of the window nicely. In that case I spot metered on the window.