Even though scatter points appear disconnected, there's some grouping going on behind the scenes. Each group of scatter points is a PointSet and colors apply to pointsets only, not individual points. By default, all scatter points belong to a single pointset, but if you start grouping points together, you will be able to control the colors better. If you want to be able to set colors on each individual data point, you need to make sure that each data point is in its own separate pointset.

One way to do this is to create an XYSeries for each point and add the series to the chart.Series. You can then set series colors via series.PEs collection. This is probably the more straightforward way.

You can also introduce a GroupBy column to your datasource instead of using series. This column can be of any type and you will get as many groups as there are distinct items in the GroupBy column. The GroupBy column index is set via chart.ScatterChart.GroupByColumn. You will also have to set UseGroupByColumn to true.