there is always a little bit of space, though not as large as you describe. a standard cherry switch and happ button has very little slop in it. (maybe 0.02 inch (about the thickness of 4 sheets of paper)) perhaps the switches you are using have a shorter than normal "peg".
if it really bothers you try cutting some plastic shims and super gluing it to the "foot" of the button. be sure to leave a little space, you don't want the button pressed down at all or you are going to run into a situation where you press down the button and the switch stays clicked and won't release.