Some undocumented changes and possible bugs managed to slip into patch 4.1.
Oracle Eggs Bugged
The Mysterious Eggs, that became available to open after three days (down from seven as of patch 4.0.3a), are bugged post patch 4.1. If the item "ripens" and becomes ready to open while the player is offline, it will disappear from the player's inventory. The disappearing egg is a known bug and developers are working on a fix, however there is currently no ETA on when the issue will be resolved. [source]
Amani Hex Stick Changes
Mojo can still be found within Zul'Aman despite the changes to the zone, but an additional change that was not mentioned in the patch notes involves the Hex Sticks.
Previously, the Amani Hex Sticks were tradable but did not persist if the player zoned out of the instance. Now the sticks remain in your bags and can even be sold on the Auction House.
Stealthy Companions
As of this patch, players are reporting that pets will stealth or go invisible with their owners. While your summoned pet will look the same and unchanged from your perspective, both you and your pet will disappear right before other players' eyes.
This seems to work with the following abilities: prowl (druid), stealth (rogue), and invisibility (mage). It does not work with the hunter ability camouflage or a night elf's shadowmeld.
Persisting Pets Getting Very Persistent
You may have noticed that not only companion pets have been more notably persistent after 4.1 was released. The persistent pet change seems to extend beyond vanity pets to some quest NPCs, such as the Orphaned Mammoth Calf, to the Innkeeper's Daughter who has been very intent on following players around!
It has been observed that players can also utilize this new feature with item-required summoned pets, such as Don Carlos' Famous Hat and Bloodsail Admiral's Hat. Although they are not classified as true vanity pets, they sure are behaving like them!
Your pet will initially disappear if you remove the item, but as long as you do not summon any other companion, if you log out and then log back in these two pets will re-appear even if you do not have the item equipped.
Intended Changes or Bugs?
We aren't sure if persisting Amani Hex Sticks was an intentional change or if it is something that Blizzard will revert. So if you are looking to satisfy a froggie-fix, it's recommended to get started sooner rather than later.
There is also no official word if companions stealthing alongside players as well as item-required persisting pets are actual features that were implemented or if they are simply bugs.