Right now, we could only think of two issues that are known to us.
Affix Widget Bug
The collapsibles inside the Affix Widget TOC and related categories/posts are persistent, so it stays closed when someone closes it. The problem arrives, when someone again opens it when scrolling at the very bottom of the page. Refreshing the page does solve this issue, but this is not expected. Right now, we couldn’t fix it. But we do not intend to leave it like this. As soon as we get some more time (and coffee) we will fix this.
Incompatibility with jQuery UI Tabs and Buttons
Since bootstrap replaces jQuery UI Tabs and Buttons, so the theme itself, in its generic form, is incompatible with jQuery UI Tabs and Buttons. Please read about the noConflict mode to work this out.