I believe it happens in all recent versions for a while now, appimages on Debian stable. I think it happens both in the “2.0” mode and the legacy one.
“New layer from visible” ends up not having the same behavior it has on GIMP and Krita (I believe even MyPaint once was like that, but perhaps my memory fails me), creating a fully opaque copy, as if you had exported a PNG and pasted it on a new layer, but rather a semi-transparent “copy” that looks like the merging of the layers when it’s above the appropriate background color. But while still on the same image, it “interacts” with it in a way somewhat analog to a “multiply” mode, increasing the saturation and darkening the original underneath.
It can be minimalistically reproduced by just painting some squiggle or shape with a color of intermediate saturation, and then attempting to creating a copy through “new layer from visible” instead of actual “copy.” You should notice the saturation immediately increased. It will only look as a copy from the visible when you move the layer out of any overlap with the painted pixels.
If you don’t have “show background” toggled on, but rather that checkerboard for transparency, “new layer from visible” will create what I believe would be more expected from it, an opaque copy, or yet, a copy with whatever is the degree of opacity of the pixels painted there.
I believe a “work-around” workflow if one needs the GIMP/Krita/maybe-old-MyPaint behavior would be to create a “real” background layer, leaving the “show background” unticked.