Water (and lava) height is different at different y-values?

Title explains what is going on, a screenshot will give more clarification if it isn't clear enough; See below.
Debug world water is at y=69 (5 pixels below a normal block); The water in the flat world are at y=64 (2 pixels below a normal block) and y=65 (3 pixels below a normal block). If the water is placed at y=69 in the flat world, the water is only 3 pixels below a normal block like at y=65. It is normally 2 pixels lower than a block.