Using the September update to Web App Builder you can use the layer symbology to appropriately colour the bars of your chart or pieces of your pie.
Unfortunately it's not working for me.
I have a registered services from ArcGIS Server 10.4.1 on AGOL and am using that in a map.
When I use the option I get black pie sections.
The layer is simple triangles with coloured interiors in ArcMap.
A limitation of non-hosted services?