What do you call tiny underdeveloped segments of an orange?

Based on the wikipedia entry that looks very much like the relevant part of the document you linked to, it is technically a conjoined twin and colloquially a navel. There is also some precedence for calling it a baby orange.

The mutation caused the orange to develop a second fruit at its base, opposite the stem, as a conjoined twin in a set of smaller segments embedded within the peel of the primary orange. - wikipedia

A Presbyterian missionary came upon it in the mid-1800s. It intrigued him that not only did the orange have a bellybutton and baby orange inside — it was sweet, and had no seeds. - Who Put The Navel In Navel Oranges?, npr.org

However, when saying that you've eaten that portion of the fruit, it's probably more socially acceptable to say that you've eaten the baby orange than to say that you've eaten an orange's navel.

Although oranges present different sizes and shapes varying from spherical to oblong, it generally has ten segments (carpels) inside.

A specificity of Navel oranges is the second cycle of carpels at the apex that leads to the apparition of a small orange inside the normal one.

You may then use the expression secondary carpel(s) when you want to refer to the underdeveloped segment(s).