Creating a 2dsphere index fails if the coordinates part of the documents has 3 coordinates. Having 3 or more coordinates is valid geojson as stated in the spec:
A position is represented by an array of numbers. There must be at least two elements, and may be more. The order of elements must follow x, y, z order (easting, northing, altitude for coordinates in a projected coordinate reference system, or longitude, latitude, altitude for coordinates in a geographic coordinate reference system). Any number of additional elements are allowed – interpretation and meaning of additional elements is beyond the scope of this specification.