According to the readme, that's a known issue that they don't plan to fix because it's funny.
ruerue244
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A member registered Jun 12, 2020 · View creator page →
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mspaintCompanion (Layers for MSPaint) comments · Posted in mspaintCompanion (Layers for MSPaint) comments
...Having some pretty significant trouble with this actually..
Switching the active layer shifts everything on that layer down,
Plus, I tried filling in a shape with the bucket tool, and it no matter how I organized the layers it was always on top of everything else.
Am I using something wrong, or is this excess jank? Is this even the right way to ask about problems with the program? Should I just use the email in the readme?