Placing water with a bucket will sometimes make the water invisible and not place where you tried to.

I'm digging out a desert and will get stuck in 2 deep holes so I place a water bucket and jump out. Sometimes when I place that water it will disappear and you have to log out and back in to see. When you log in the water will be in a hole around your area but sometimes as far as 10, 20, or 30 blocks away. It's hard to recreate but it happens somewhat frequently.