To its credit, Bob's Burgers didn't show any indigenous humans. What it did show was cavemen, Vikings, and pioneers in a covered wagon. All had light-colored skin, so the only racial group on display were Caucasians.
This is a bit silly, since natural history museums generally don't feature Vikings or pioneers. It seemed like a contrived effort to be "politically correct."
But the show undercut this by presenting one boy's list of exhibits with "boobs." The list read:
East Timor boobs
For starters, the boobs list implies that indigenous people are nothing but sexual objects of interest. Whoever wrote this episode probably learned about these people from old National Geographics.
The thatched hut sends a similar message. Namely, that indigenous people are part of nature, not part of humanity. That they're closer to trees and monkey than they are to doctors and lawyers.
Summing up Bob's take: Wild animals = primitive white men = modern indigenous people. In other words, "Eskimos," Amazon Indians, and other brown-skins belong in a museum with extinct species (dinosaurs, woolly mammoths) and civilizations (Egyptians, Vikings).
Bob's Burgers suffers from the same mentality seen in Indians in Natural History Museums, Indians in Bailey at the Museum, and Eurocentrism in Night at the Museum 2. That's stereotypical if not racist.
For more on Bob's Burgers, see Navajo Mask in Bob's Burgers.