YUI().use('charts', function (Y) {
var data = [{date: '2011-01-02', key1: 10, key2: 5, key3: 0},
{date: '2011-01-03', key1: 5, key3: 4},
{date: '2011-01-04', key1: 2, key2: 4, key3: 4}];

var chart = new Y.Chart({
dataProvider: data,
stacked: true,
type: 'column',
categoryKey: 'date',
render: '#chart'
});
});

If the chart div is 640x400, you'll see that the key3 in the first column is drawn with some heigh under the X axis and the missing key2 will appear as empty space and with an extra ghost column in
the second data point.

I would expect missing keys to be interpreted as meaning 0 (at least in the column/stacked case) and value of 0 not getting any height.