1. Install MsCatSelect (https://www.mediawiki.org/wiki/Extension:MsCatSelect)
2. Open the wiki with IE 9, 10 or 11.
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 played with $wgCachePages and other cache settings to try to prevent client-side caching, but the bug persists. This may be a IE bug, rather than a MediaWiki or MsCatSelect bug, because in Chrome and Firefox it doesn't happen. Also, if you switch to IE debug mode then the bug disappears, which further supports the idea that IE is caching things it shouldn't, as the debug mode probably disables caching.

However, here is the strangest part: SmartK and me tried to reproduce this bug in two wikis, both with IE 11. I was able to reproduce it in only one wiki, while SmartK was able to reproduce it in both! The only apparent differences between the wikis is that the one where I COULD reproduce the bug had PHP 5.3 and a https domain, while the other had PHP 5.4 and a http domain. But again, SmartK could reproduce the bug in BOTH wikis. So really, I don't know where the bug comes from. This is a very erratic bug, the only clear thing is that it's IE and cache related, but more testing is needed to pin down the cause.

Small update: We think this bug was introduced with MediaWiki 1.21 or 1.22. We still have it today in stable MW 1.24 but could not reproduce it in MW 1.25. Maybe this helps...

Can someone else take a look? It's a very annoying bug for MsCatSelect, and would be great if it could be fixed somehow, even if IE is to blame.