Json can have arrays within arrays. yql is not handling these correctly. This means that GeoJSON files for example cannot be used within yql.
For example, I have put the sample GeoJSON file (http://geojson.org/geojson-spec.html) at http://maps.peterrobins.co.uk/files/geojson.json
If you fetch this with http://query.yahooapis.com/v1/public/yql?q...amp;format=json the point coordinate is correct, but the linestring and polygon coordinates are not. Valid GeoJSON has been converted into invalid GeoJSON.