It's expected to behave like that, Maya doesn't know what you plan on doing with it. Typically I run an edge loop first along the side, so I have the geometry for knocking out that side face. After the extrude, snap the face down to the loop: Move tool, hold d and v to adjust pivot -and- snap to border vertex and release.…
Make sure to Freeze Transformation>Center Pivot>Delete all History every time after moving the mesh into place and before binding it to the bone using Smooth Bind. Also, are the masks finished? They are the ones responsible for the shading to work in-game. Also make sure that you're saving them as 32bit TGA and that you…