The first command returns a document which is outside of the given circle. Decreasing the radius doesn't help.
> db.aggregates.find({position:{$within:{$center:[[46.16760025, 8.79330351666667],0.00001]}}})

{ "_id" : ObjectId("4c07ca39f18d653fb9000001"), "position" : [ 46.16997015, 8.799318833333333 ] }

The geoNear command returns the same object but calculates a distance which is higher than the radius used in the above command.
> db.runCommand(

{ geoNear : "aggregates" , near : [46.16760025, 8.79330351666667], num : 1 }

);
{
"ns" : "myway.aggregates",
"near" : "1100100000010100101100100010000011010000101110010100",
"results" : [
{
"dis" : 0.0064640792077458676,
"obj" :

{ "_id" : ObjectId("4c07ca39f18d653fb9000001"), "position" : [ 46.16997015, 8.799318833333333 ] }

}
],
"stats" :

{ "time" : 0, "btreelocs" : 0, "nscanned" : 1, "objectsLoaded" : 1, "avgDistance" : 0.0064640792077458676 }

,
"ok" : 1
}
>