Using KiCAD 6.0.2. This seems like a minor bug. I would not expect the layer alignment target to prevent zone filling in that area. Seems like it is acting like an edge cut.
I don’t know that I really need the alignment target in this case, so I will just remove it. I just didn’t think the behavior was correct and thought I would share to see if anyone agrees or has a further comment.
The layer alignment target is plotted on all layers (which is obviously necessary to align them) so it should be outside the board area. Otherwise you’d get a crosshair on all copper, silk and other layers on the board, which is pretty stupid.
You typically don’t need layer alignment targets, they’re obsolete. These would be necessary to align the layers if you distribute a board design on paper or something.