I've had the same issue. The problem is that you're not using a multidate picker, but a range picker. The current datepicker does not have a method to get the dates from all pickers.
That's not a big problem, since each date can be easily obtained by using another function: getDate
I've made a jsfiddle to get the dates and count the number of days between two dates. You can see the full example here: http://jsfiddle.net/svierkant/7abqJ/1/
$(document).ready(function()
{
$("#datepicker").datepicker({
format: "dd.mm.yyyy",
multidate: true,
calendarWeeks: true,
autoclose: true,
todayHighlight: true,
startDate : new Date("2014-02-01"),
endDate : new Date()
}).on("changeDate", function(e){
$begin = $('#start').datepicker('getDate');
$end = $('#end').datepicker('getDate');
});
});