Perhaps this is by design, but I would expect the autoexplore option to send the units onto the various goody huts (treasure, bones, etc.) on the map, like it does in Civ 4 and GalCiv 2.
From my tinkering last night, it seemed like the autoexplore explicitly avoided entering these squares, and instead focused only on uncovering the map. I had only tried it with the Sovereign however.
