During the traveling montage Po and his father endure on their way to the secret panda village, they pass by two large stones that sit on a equally stone like terrain and are slanted toward the right of the screen. Shrek and Donkey pass by these same stones on their way to Fiona's castle in the first Shrek (2001) movie.
In order to get a feel for how pandas live, the filmmakers went directly to China's biggest panda preserve in Chengdu. While there, the filmmakers noted that pandas rolled to get places and incorporated that into the film.
On General Kai's chain belt with the chi amulets of masters that had died are a number of masters that he did not use: among them can be seen the amulets of Masters Elephant, Hippo, Thundering Rhino from the second film, Lizard, Komodo, Frog, Crab, and Tai Lung himself, indicating that Tai Lung was banished to the Spirit Realm when Po used the Wuxi Finger Hold on him in the first Kung Fu Panda (2008) film.
Kai's name was initially going to be Tian Sha, which means "ferocious (spirit) from heaven", and the characters separately mean "heaven" and "evil spirit" respectively. In the Chinese dub of the film, his name remains Tian Sha.
Four of the Jombie Masters can be seen as they appeared in life in Po's room: Master Porcupine was gray with orange robes, the Master Badger Twins were black with yellow robes, and Master Gorilla was shown to resemble Lord Shen's gorilla warriors from Kung Fu Panda 2 (2011).
Kai's original appearance would have had him with four arms, to resemble a character that was drawn in development for the first Kung Fu Panda (2008) film, known as the "Four-Armed Yak Demon God on Fire" who initially would have served as a member of Tai Lung's gang.
This is the first Kung Fu Panda film where Tigress wears different clothes. In the first and second films, she wore a red qipao with golden vine patterns and black pants. In this film, she wears a long-sleeved yellow tunic with red vine patterns and black pants.
A deleted scene would have featured Master Shifu speaking to the statue of Master Oogway, expressing his concerns about how the world would be consumed in darkness, and how Shifu might need a hobby or a girlfriend.
Wayne Knight who voiced one of the Pandas in the Panda Village had also been in the first Kung Fu Panda (2008) film as the voice of the Enemy Chief from Po's Dream at the Start of the Film that Kai had been inspired from.
A subplot that was ultimately cut from the finished film was that Po, Shifu, and the Furious Five would have held off the jombie masters at a standoff, at which point the undead masters would run off, rather than to dissipate into green orbs of light as they had in the finished film, but not before one quick skirmish in which Master Porcupine fired three of his quills from his bow, one of them hitting Mr. Ping, who dove in front of Po to take the shot. In that subplot, Li Shan would have tended to Mr. Ping's injuries and Mr. Ping would have blamed himself for being a burden to Po, partially due to the toxins of the quill affecting his brain.
Two deleted scenes from the film would have featured Po bringing his dirty laundry to Mr. Ping to wash, taking off his pants as he did, and accidentally exposing his rear to the Furious Five, who were reviled; and a scene in which Mr. Ping brings back Po's dirty laundry to his barrack at the Jade Palace. In that scene, Mr. Ping voices his displeasure at Li Shan being included as one of Po's father figures after only being in his life for a few months, and Mr. Ping attempting to right his wrongs towards Li Shan by making plans to prepare an expensive feast for him.
In the deleted scene in which Mr. Ping visits Po at his barrack, the wok that struck Tai Lung in the face from the first film can be seen, as well as a drawing of Po (which he likely did himself) with six-pack abs, as well as a poster of the late Master Thundering Rhino standing in front of the Tower of the Sacred Flame from the second film.
Tai Lung has appeared in a way in the three films, in Kung Fu Panda (2008) he is the main antagonist, in Kung Fu Panda 2 (2011) he is briefly mentioned and appeared in a flashback and in Kung Fu Panda 3 (2016) Po has a toy with the figure of Tai Lung and Kai has a Chi stone with the shape of him.
In the opening sequence when The Dragon Warrior and the Furious Five were running through the valley, Po jumped to the sky and kicked through a cloud that has the shape of a rhino. This action was made to look like Po just beheaded the rhino, which is a preempting the inevitable ending of the Dragon Warrior defeating the villain Kai.