#3
I was working with transparent pngs and noticed that on saving paint net was injecting random black pixesl in / around where I had cut unwanted graphic away.
In the paint edit window the glitches did not exist but they existed and persisted on my output file throughout every save, to get around this issue I added a layer below the alpha png, merged down, saved and seem to fix the issue as a sort of work around, annoying though.