Water and other objects (traps, exits etc.) need to be placed at multiples of 8 in the x-direction and 4 in the y-direction, otherwise they won't work as intended. It's a limitation of the game rather than a problem with the editor. Lemmix allows you to place these anywhere, but the triggers (the parts that interact with the lemmings) are fixed to 4x4 grids, so you could end up with (for example) lemmings drowning above or beside a body of water.