Indeed, and they never will. These slight differences are between a few generations; evolution has operated over countless thousands of generations. Each generation is slightly different to its predecessor, to the extent that every daughter is the same species as her mother. But, if you compare distant ancestry, that same daughter is not the same species as her far-distant grandmother. Furthermore, that distant grandmother will have countless thousands of living descendants, which are themselves grouped into separate, distinct species.
Consider this grandmother to a member of the first species of mammal, species M. This grandmother, and all other members of species M, are long dead, obviously. Their descendants exist in each generation as a group of individuals, living and breeding. Somehow, they split into genetically isolated groups - perhaps a river has formed, and they can't cross it.
So any new genetic material in one group will spread to all members of that group, but not to the others across the river. So, over time, the two groups become more and more genetically isolated, and it becomes less and less likely that sperm from one group will be able to fertilise ova from the other.
Eventually, they can't interbreed, and those two groups are two different species - descended from the same species, but now different species.
Anyway. Even though the descendants of fruit flies will always be fruit flies (and, thus, insects, arthropods, animals, etc), those descendants could be completely different from the original fruit fly species, and from each other. Giraffes and whales look completely different from each other, and from their common ancestor, but they're still related.