Minimize noise in drawings; keep only intended shades

[rich2005]

There is certainly a specking of odd pixels in the posted image. Why ? I do not know from your procedure. 

Using paths, no need for stroking and bucket fill. Edit -> Fill Path and untick the anti-aliasing option.

You should possibly keep each AOI on its own layer, until your final export.

This looking at your posted png image, a bit of analysis, a bit of a fix.  About 5 minutes: https://youtu.be/--_IhNoJDMI