Looking at this, dimple doesn't currently support null values quite as it should. If there is a null in your data it will fail the check for a numeric field and treat it as a string field, which means when you use it for a measure axis you will get a distinct count of values rather than an aggregate total. I will fix that in the code base but in the meantime - if you are able to treat nulls as zero in your dataset - you can hide them after drawing:
...
chart.draw();
series.shapes.style("opacity", function (d) {
return (d.yValue === 0 ? 0 : 0.8);
});
Here's a fiddle to show what I mean: http://jsfiddle.net/GeLng/2/
Edit, I've just noticed you are doing 2 category axes which changes it a bit. You can still remove the bubble and you can treat it as null, you don't need to worry about converting to zero, but I'm not sure of a way to avoid there being a null space on the y axis: