I think I know what you mean, and if I'm right, it's just a matter of being careful.

When you extrude faces, MAYA does create new faces edges and vertices, so you can pull the faces out and not affect the connecting faces, because they're not sharing the verts and edges any more.

Sometimes what happens is when you extrude, perhaps you deselect unintentionally and on instinct extrude again. This is what I personally call a "double extrude." (<--I'm charging two cents from anyone who uses that term from now on, hehe. Kidding of course ). When you extrude a face/faces, the new faces edges and verts are created even if you don't scale, pull or rotate the original face you extruded. So if you do it again, you have twice as many as you wanted.

Try it to see what I mean: Extrude a face and click anywhere else in the screen to deselect. Then grab that face and pull it out with the normal move tool, it will still be pulled out without affecting the adjoining faces, meaning that new faces and vertices and edges were already created

Another problem might be your mouse is too sensitive and when you click the button on the shelf, it does a double extrude. Now this was longer than I thought, but, I hope it helps.