Is there any genetic similarity that defy evolution theory?
Your question seems rather confused to me, I don't quite understand it. Below I try to explain some stuff, I am not quite sure it would help you finding the answer to your question. Let me know if it helps you and how I can improve this answer.

While natural selection selects for a given allele (gene variant), mutations create new variation. And because of this process of mutation there is genetic pattern in species D that would cannot be found in species B (assuming that we have the DNA of species D). But what is similar between B and D were probably also present in their common ancestor B. The exceptions are molecular convergent evolution and horizontal gene transfer (natural of artificial).

Because of common ancestry …


Humans have similarities with pigs


Example: endothermic amniotes

Humans have similarities with a bug


Example: bilaterial symmetry

Humans have similarities with jellyfish


Example: Heterotrophy

Humans have similarities with an oak tree


Example: We have mitochondrias

Humans have similarites with any living things on earth!


Example: Genetic information is hold into a DNA/RNA molecule.





If you might observe that D is genetically speaking more similar to C than to E… This can be due to:


Horizontal gene transfer (artifical or natural)
The mutation rate (or ability to fix mutations) in one lineage might be greater than in another lineage.


For example, if lineage E underwent many mutations, they might be genetically speaking have accumulated many difference compare to D, way more than the number of difference that D has with C.

The phylogeny might be wrong
There might have had some convergent evolution.


Think about fishes which opsins in the eyes need to be adapted to the amount of light which depends on the turbidity of the water. After the three lineages splitted, the change of envirronment might have occured the sequence AATGATCCT suddenly became beneficial. Only two lineages had the chance to produce the right mutation. Or maybe lineage E live at low depth and therefore it doesn't need this mutation because there is enough light at low depth anyway.



Therefore, one should not expect a common ancestor to be the arithmetic mean (supposing it means something) of the current species. And one should not expect that two closely related species on the tree of life should necessarily be more genetically similar to each other than any of the two to a third species.

Note that the phylogeny is constructed mostly based on genetic data. Which makes that two closely related species (on our tree which is not necessary the absolute tree of life) are (almost) necessarily more genetically similar (it is kind of a definition then).