This happens when user colors by a clinical attribute in the plots tab and filters down categories. If I select only a few of the metastatic sites on the vertical axis, the legend does not update and still shows all possible values and colors. It is very difficult to match the colors on the plot to the colors on the legend this way. (see example, you need to use filter categories option)

Ideally only colors present in the plots should be included in the legend. Alternatively, the relevant entries in the legend could be highlighted by default if they are present in the plot.