Using 2 libraries at same page: jQuery UI and Twitter Bootstrap:
If you are only using the dropdown plugin of Twitter Bootstrap, you don't need the .button()
plugin.
Go to the customize bootstrap page and unselect all jQuery plugins, then choose only the dropdown one. You could also unselect some of the CSS if you want.
.button
to something like .bsButton
in the bootstrap-button.js file (or find this section in a non-minified version) - not tested.