There are a lot of people who contribute themes. These are not made by the makers or developers of the WP core. There are a lot of themes that unfortunately do not validate. They have mixed HTML and XHTML together on the same page or use depreciated tags etc. WP currently does not require a submitted theme to validate according to W3C standards. (maybe an idea for the future)
IE has always had odd behavior compared to the other browsers. Fortunately there are conditional comments. Read the following posts they'll shed some light on how that works.