When you cut glass pieces when making a pendant with two pieces of glass fused together, make the top piece of glass a fraction of an inch larger than the bottom piece. Do this so that the top piece will melt completely over the bottom piece. That way the bottom piece of glass is totally encased by the top layer. For this "look", you do not want to have any of the bottom piece of glass sticking out from under the top piece of glass unless your design was meant to look that way!
If you accidentally cut the top piece too small and the bottom layer is not covered by the top layer of glass, it is possible to use a glass grinder to remove that area. Once completed you'll have to refire that piece of glass to fire polish the edges again.
As you can see in the photo below, the top clear cap glass is slightly wider than the bottom black piece of glass.
Sample image from http://www.craftstylish.com/item/5522/a-beginners-perspective-on-fused-glass-jewelry/page/all