The Mootools framework that UltraCart's javascript checkout API can be incompatible with other frameworks. We've tested and built checkouts with the JQuery framework being used as well. In order to use JQuery with Mootools you should include it in your page after Mootools and use the following code to object your JQuery instance.
var $j = jQuery.noConflict();
This applies to version 1.0 of the Checkout API. Versions 1.2+ only use jQuery now. mootools is not used.