You can prevent that. You can fix any object's offset in the layer settings, by going to the individual object's settings and clicking on the blue underlined offset displayed there. With that you can make sure that the bottom of the trunk is the object's "anchor"; in other words the block that gets placed directly on the ground at the object's location. On the same screen you can set the collision settings so that the trees don't intersect each other. Configured correctly a custom object layer is an excellent way of placing trees.
Really? Please see that