I recently made a map as a test because I learnt how to add water. This si the second time I have used water in a map. Anyway, ingame I spawn and everything is alright, then I walk over to my lake and look at it... Its normal. Then I look more down into the deep water and the map crashes. Very weird. Its like it can't handle that much detail?

Explain how you added the water (following this tutorial?) and get an error log. How much water surface does your map have? Too much can cause a crash.

Does it still add a water panel if you click again over one panels place?

No, it ignores the second click.

you didnt add it at two different heights in the same place did you....i know that has crashed it for me before.

You can't have it at two different heights in any place.