The FilteringSelect uses a unicode annotation character to highlight the matching part of the suggestions. I see the same thing here, so I guess IE has a problem rendering them and it slipped past the dojo tests.
No idea how to fix it, but as a temporary measure, you can set the FilteringSelect's "highlightMatch" to "none".
Edit: It seems to be a known bug related to the build tool/shrinksafe: http://bugs.dojotoolkit.org/ticket/15969