There is a bug in a dependency configurator.
I downloaded YUI 2.9.0 version with configuration below:
http://developer.yahoo.com/yui/articles/hosting/?animation&autocomplete&button&calendar&carousel&charts&colorpicker&connection&connectioncore&container&containercore&cookie&datasource&datatable&datemath&dom&dragdrop&editor&element&element-delegate&event&event-delegate&event-mouseenter&event-simulate&get&history&imagecropper&imageloader&json&layout&menu&paginator&progressbar&resize&selector&simpleeditor&slider&storage&stylesheet&swf&swfdetect&swfstore&tabview&treeview&uploader&utilities&yahoo&yahoo-dom-event&yuiloader&yuiloader-dom-event&MIN&norollup
The problem is in Selector Utility script. Initialisation script is executed in global scope not in a closure. It cause that Selector variable is overriden in global context which causes conflicts with prototype library.
In version 2.8.1 it was working right.
Additionally, Selector Utility script is added twice in a generated script
