When painting colour over colour (in the same layer) the resulting opacity of the pixel is correct but the residual colour and new colour elements are inverse and less opacity reduces the amount of the original colour used instead of reducing the amount of the new colour used.
Steps to reproduce
New sprite
Flood Fill with any colour
Select a contrasting colour
Select default brush tool
click once
Notice how the new colour is applied more in the corners where the opacity is reduced.
When painting colour over colour (in the same layer) the resulting opacity of the pixel is correct but the residual colour and new colour elements are inverse and less opacity reduces the amount of the original colour used instead of reducing the amount of the new colour used.
Steps to reproduce