In this book, Diamond uses the word "fragmentation" to mean the opposite of "unity" or "homogeneity." In other words, when fragmentation happens, a continent or a region has many different types of some attribute rather than just one.
For example, Diamond speaks in Chapter 2 about the fragmentation of some Polynesian islands. Here, he is talking about geographical fragmentation. Islands like these are ones where there was some sort of geographical feature like a mountain range that split the island up into distinct little parts. This is the opposite of an island that is unified. As another example, Diamond talks at times about linguistic fragmentation. Here, he means that a region has many different languages spoken in various parts of that region. This is the opposite of a region that is unified in terms of the language that it speaks.
So, "fragmentation" means that a place is in some way split into sections that are in some important way different from one another.