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I'm trying to edit a 16x16 texture. I selected a circle, but when I try to use the pencil on it near the edges of the selection, it draws a semi-transparent pixel instead of the opaque one I want it to. It works normally in the middle. Is there a way to fix this?

By default the Ellipse select has anti-aliasing so border pixels are partially selected, and so partially painted.

Either redo the selection after un-ticking the Antialiasing option in the Tool options, or use Select>Sharpen on your current selection.