The error is thrown by a call to div.getElementsByClassName("e") in sizzle.js.
HTMLElement.prototype.getElementsByClassName is overwritten by prototype.js and it uses $ which is overwritten by jQuery. The result is that jQuery can't finish initializing and prototype is also left broken.
window.$ and window.jQuery is exposed at the end of core.js before the feature detection code in sizzle.js.
// Expose jQuery to the global object
return (window.jQuery = window.$ = jQuery);
If I move the exposure code to the end of outro.js and call jQuery.noConflict(true) right after the jQuery code, then both prototype and jQuery will be fine.
I know why the exposure is advanced to core.js but maybe there is a better way to avoid the conflict. e.g. Put sizzle.js code to the beginning because it doesn't rely on jQuery anyway.
The discussion about this issue in the dev forum: https://forum.jquery.com/topic/jquery-conflicts-with-prototype-and-the-fix