Some of what could be causing the "bleed over" bits shown in the picture on the right (#1) are caused by the Anti-Aliasing (feathering) that is occurring in #2 and #3. There might be a hitch somewhere in the reading of the image file on the game side of the house.
Essentially what is happening is your 2D program is calculating the proper blend method between the red (foreground) and the background colors, this can lead to erratic end results depending on your brush/tool and eraser settings. Try turning off "feathering" or "Anti-Aliasing" in the tool that you are using (ie... Paint bucket(fill), Line, Shape, etc...) and in the eraser tool as well. Then see if the problem has been resolved.
