niri/wiki/FAQ.md

Why is the border/focus ring showing up through semitransparent windows?

Uncomment the prefer-no-csd setting at the top level of the config. Niri will draw focus rings and borders around windows that agree to omit their client-side decorations.

By default, focus ring and border are rendered as a solid background rectangle behind windows. That is, they will show up through semitransparent windows. This is because windows using client-side decorations can have an arbitrary shape.

You can also override this behavior with the draw-border-with-background window rule.

Why is the Waybar pop-up menu showing behind windows?

Set "layer": "top" in your Waybar config.

Niri currently draws pop-up menus on the same layer as their parent surface. By default, Waybar is on the bottom layer, which is behind windows, so Waybar pop-up menus also show behind windows.