The fix for bug 39180 ( https://gerrit.wikimedia.org/r/20472 ) broke UploadWizard in IE, because it uses an iframe to submit a form that includes a file upload input. This has to be done with a form submission rather than AJAX because it involves a file upload, and it has to be done in an iframe to prevent the browser from navigating away from the page. In modern browsers, it uses a combination of FileAPI and binary XHR so an iframe isn't needed, but in IE these features aren't available so it falls back to using an iframe.
I am now working around this on the live site by setting $wgApiFrameOptions = 'SAMEORIGIN'; for all wikis that have UploadWizard. We couldn't reach Chris to get his input on this, but RobLa approved it on his behalf.
Filed this bug because the above is a temporary hack and we should discuss a more permanent solution.