When exploring a planet with Mako, there are usually three points of interest each of these types:
Fallen spacecraft, contains story object. Sometimes these are Prothean objects
Minerals that can me marked for future mining by the Alliance (pressumably). For some reason, this requires "hacking" them.
A quest mission, typically a structure that can be entered so you can kill everyone inside.
All of those typically appear on map. Are there any objects that are not highlighted on the map? Or are any of the POI types mentioned above sometimes hidden from the map, requiring manual survey of the terrain?