I take the following steps:
Click 2 overlapping features from 2 different featLayers.
Popup auto-selects and highlights map.infoWindow.features[first object]
The popup content is actually from map.infoWindow.features[second object]
After you navigate to the second graphic and back, the popup corrects it's self??
here's an example using esri data: http://jsfiddle.net/92Q2G/1/
Any advice? Thanks.