Thread:Extension talk:WYSIWYG/IE11 with MW 1.22.0 + WYSIWYG extension: Existing category definitions will corrupt after after page has been saved/reply (13)

So WYSIWYG should already be enforcing the Compatibility Mode: to ensure that, you should reset your browser's Compatibility settings and check that IE is defaulting to Compatibility Mode.

Moreover, could that setting be edited by the extension itself (e.g. with a hook)?