Drupal 7 views admin redirecting to json returned after changing jquery version
You can't just upgrade the jQuery in the misc directory. You will get many many problems.

If you want to update jQuery because a specific plugin you want to use requires it, I would recommend the jQuery multi module.

However if you want your whole site to use a newer version, use the jQuery update module.
Currently though, the jQuery update module only supports up to jQuery 1.8.2.

In my experience using jquery update with versions above 1.5 was still too buggy, however those issues are claimed to have been fixed recently, so if you use the latest dev version it will apparently work.

However, you need 1.9 so jquery update isn't an option yet.

If you need 1.9 for a library (I assume that is probably the case), I would say use jQuery multi (I have successfully used it to run a bunch of things off on top of backbone.js and it has been working without issue for a long time now).