When the enraged hippo rears up, Homer exclaims "A hungry hungry hippo!", a reference to the popular board game Hungry Hungry Hippos. Incidentally, one of the four hippos in the game is called Homer Hippo.
Dr. Joan Bushwell is a parody of Dr. Jane Goodall, an English zoologist who became famous worldwide for her research into the behavior of chimpanzees.
While in the jeep, the sun is rising and Marge shows the kids the animals, a nod to Disney's The Lion King. Also, Pride Rock can be seen in the distance.
When Marge remarks Dr. Bushwell hid diamonds on the soles of her shoes, it's a gag to the Paul Simon song "Diamonds on the soles of her Shoes"
A Rhino hatching an egg and the Giraffe coming out of the ground are now in Tapped Out, in the Moe's Ark Event.
For a brief moment when Bart is eating worms, his tongue is green.
When Dr. Hibbert looks at Maggie's insides through the X-ray, the "Time" in Time Magazine is digitally blurred out (possibly for copyright reasons). In a close-up of Maggie rolling her eyes, the "Time" in Time Magazine isn't blurred.
The geography is inconsistent. The Simpsons landed in Tanzania, but later on in the episode they fell down the Victoria Falls, which is on the Zambia-Zimbabwe border, both countries laying southwest of Tanzania, with Zimbabwe having no border with Tanzania at all. Shortly afterwards, Homer tells Bart to climb Mount Kilimanjaro, which is in northern Tanzania.
Also the river that leads to the Victoria Falls doesn't go through Tanzania at all so it would be physically impossible for the Simpsons to have gotten there by boat (or, in this case, shield).