Clutch in or out while waiting at a light?

That sounds like a poor quality clutch master cylinder. Sitting with the clutch in at a light should not hurt the clutch master cylinder, but it does accelerate the wear on the throwout bearing.

It does not matter a lot, but if you want to try to ensure that your throwout bearing lasts as long as your clutch, it is best to slip the car into neutral and release the clutch at a long light.