When you click in an empty “color square” (swatch) Krita puts there your current active color.
If it’s not the color you desire in the palette, first you have to select the unwanted color, than you can:
- Remove it via the “trash” icon
- or Edit it via the “pen” icon
Via the “pen” icon you can edit also the name and other things of the swatch.
It works for me, I didn’t notice the bug cause I always put new colors with a click in empty squares and use “Remove” or “Edit” for all my needs.