If you are using custom scripts that are not compatible with the latest version of jQuery then you can add this in layout.master:
<portal:ScriptLoader ID="ScriptLoader1" runat="server" IncludeJQueryMigrate="true" />
This will include an extra script that restores the things that have been removed from jquery 1.9
Artisteer skins need this now because their script is not yet compatible.
If you are using well known jquery plugins you might check for the latest versions to see if they have been updated to jQuery 1.9.
I updated several plugins included with mojoPortal including superfish, colorbox, and cycle plugins.
If you are using a menu with mojosuperfish.js you can make it compatible by changing to mojosuperfish150.js
Hope that helps,