1. Install MsCatSelect (https://www.mediawiki.org/wiki/Extension:MsCatSelect)
2. Open the wiki with IE 9 or 10.
3. Edit a page with 2 or more categories.
4. Uncheck one category from the checklist introduced by MsCatSelect and save.
5. Edit the page again.
6. Notice how the category just removed appears again, as if the last edit wasn't saved. However, if you clear the cache (by refreshing for example) the category is gone.
My speculation is that IE is caching parts of the interface that it shouldn't be. I've tried setting $wgCachePages to false to prevent client-side caching, but the bug persists. This may be a IE 9-10 bug, rather than a MediaWiki or MsCatSelect bug, because in IE 11 the bug is gone and in Chrome and Firefox it never happened. Also, if you switch to debug mode in IE 10 then the bug disappears, which further supports the idea that IE is caching things it shouldn't. But can someone take a look and confirm this? It's a very annoying bug for MsCatSelect, and would be great if it could be fixed somehow, even if IE is to blame.