The Cleanup feature lets you remove unwanted geometry from a polygon mesh (for example, zero area faces or zero length edges). You can also tessellate faces that may be valid within Maya, but not in a game console, such as concave faces, or faces with holes.
This can occur when you set the Cleanup options to perform multiple cleanup operations on a mesh in a cascading way.
If this situation is likely, it is recommended you run the Cleanup feature multiple times and turn on the Non-Manifold Geometry option in the Remove Geometry section only on the last iteration.