In ArcGIS Online, both Web Maps and Web Mapping Applications have a default color set for selected polygons. The polygon boundary is highlighted in cyan and the polygon highlighted in a semi-transparent brown. (See image below)
While clearing the selection will remove this highlight, many inexperienced users may not think to do that. Also experienced users with concerns regarding color choices may worry changing the color of a thematically colored layer is unacceptable.
Some Web Mapping Application templates do change this, however, I have found they then change too many other things to be acceptable. It seems like it would be easy to allow selection color to be controlled in all Web Maps and Web Mapping Applications.