I just ran into this same issue. I was able to solve it by adding a container attribute to the div.
$('#myDatePicker').datepicker({
container:'#myModalId'
});
or if you are using the “lazy load” method as I was:
<input id='myDatePicker' data-provide="datepicker" data-date-container="#myModalId">
Reference : http://bootstrap-datepicker.readthedocs.org/en/latest/options.html
Hope it helps someone else!