FIX DISCOLOURED POLYGON ERRORS
01 LOCKED VERTEX NORMALS
One of the first things I check when I experience an issue like this are the vertex normals. Occasionally, when importing an OBJ file or other non-native data file, the surface normals can become locked at an incorrect angle, making the vertices and surrounding polygons appear darker. Thankfully this is probably one of the easiest issues to correct, all you need to do is select the model and use the Unlock Normals option in the Mesh Display menu.
02 SCULPTING ARTEFACTS
This issue is possibly more of a bug in Maya, but you may have found yourself working with Maya’s sculpting tools and when you finish, some polygons are left black. They may vanish when you disable the shader, but this just hides the issue as they appear again when the shader is enabled. I’ve tried many things to correct this problem, but the only approach I’ve found that works is to export the model as an FBX. This will strip out that unwanted data.
03 VERTEX COLOURS
Another feature that can cause issues with your models are vertex colours. Rather than having distinct black patches the whole model could appear to be the wrong shade or you could experience patches of other colours over its surface. To clear a model of any colouration you would need to use the Apply Color tool which is found in the Mesh Display menu. Here you can simply choose to remove all the colours from the model, which should fix the issue.
04 FLIPPED POLYGONS
One final thing to check would be the direction the affected polygons are facing. Polygons can face both ways and depending on your display settings, this may not be immediately obvious. First, check that Backface Culling is enabled in the current viewport. This will make all the polygons one sided so you can clearly see if this is the problem. If it is, you can then go to the Mesh Display menu and use the Conform tool, which will check all the polygons are facing the same way.