I am not sure if its my service or some kind of buffer setting is turned out, but when I add my FeatureLayer to my map, the popup that is generated shows the information for the feature that is at the top. So basically shape 1 and shape 2, shape 1 is above shape 2, and when you click up to half way in shape 2 you get the information/attributes from shape 1.
Update: Seems to not be so bad when the url points to a MapServer instead of a FeatureServer.