When $wgArticlePath is set to '/$1' for friendly URL's, $wgUsePathInfo cannot also be used. Many installs use both of these in together so that the friendly-rewrite rules map to a PathInfo based request so that un-encoded ampersands and question marks can be used in article titles which aren't allowed if using query-string.
What's happening is that the new extractTitle method in the WebRequest class is returning a title value like "Wiki/index.php" when the request's title is in the query-string. I suspect that it should not be returning anything in when the title is in the query-string and should only be returning a title key when the request is PathInfo-based.
To fix it temporarily on a number of 1.11's that it's happened to I've replaced the WebRequest constructor with the 1.10 version, and made the interpolateTitle method return before doing anything. I've put more detail at http://www.organicdesign.co.nz/MediaWiki_1.11_title_extraction_bug.