Except that we see the same genes involved in the same function in unrelated organisms… people call it convergent evolution, parallel evolution etc.
There are papers which say the appendix came and went 32 times in mammals… and it’s not only the appendix.
The eye seems to have evolved several times. Though some instances are that of different mechanisms creating similar result, some are homologous genes/biomolecules etc.
On the other hand we have things like hair/fur in mammals which remain constant through 100’s of millions of years… even though there are close alternatives like scales, feathers etc which could have arisen, considering the diversity achieved by this group.
Considering that species change by both dropping as well as gaining traits, it’s very difficult to see how some specific traits remain conserved for immense durations while others don’t (and it’s this consistent conservation across time involving immense change in other genes which creates nested heirarchies)… and even these traits are not common throughout life… they vary from class to class…
Edit: one example for a naturally occurring nested heirarxhy in biologicals systems is embryo development. It leads to cells that occupy a specific niche in the body through a process involving heavily regulated/controlled variation. That’s the only way to get a nested heirarchy. Control over the process of change.