It should have been a solution:
The word phylogeny refers to the evolutionary history of an organism. The word was coined by German Darwinian biologist Ernst Haeckel several years after the publication of On the Origin of Species. Evolutionary biologists have proposed phylogenies based on homologies in fossils, but as we have seen, there are problems with both fossils and homology. With the rise of modern molecular biology, evolutionary biologists have increasingly sought to base phylogenies on molecules such as proteins and DNA.Jonathan Wells, “Top Scientific Problems with Evolution: Molecular Phylogeny” at Evolution News and Science Today (February 14, 2022)
And then what happened?
Molecular comparisons are complicated by the problem of alignment. DNA sequences in living things typically contain repeated and/or deleted segments, so it is often unclear where to line them up. If two sequences can be aligned in more than one way, then any comparison will depend heavily on what alignment the investigator chooses. And when many sequences are compared, as they are in molecular phylogenies, the problem becomes much worse.Jonathan Wells, “Top Scientific Problems with Evolution: Molecular Phylogeny” at Evolution News and Science Today (February 14, 2022)
So discrepancies were feature, not a bug:
And the problem has only grown worse as more data have accumulated. In 2005, three biologists who compared 50 DNA sequences from 17 animal groups concluded that “different phylogenetic analyses can reach contradicting inferences with [seemingly] absolute support.”5 In 2012, four evolutionary biologists reported “incongruence between phylogenies derived from…different subsets of molecular sequences has become pervasive.”Jonathan Wells, “Top Scientific Problems with Evolution: Molecular Phylogeny” at Evolution News and Science Today (February 14, 2022)
We can assume common ancestry as a starting point for from molecular phylogenetics but we can’t use such a system to prove it.
You may also wish to read: Jonathan Wells rates homology as one of the top scientific problems with evolution theory. Similarity of features is taken to be due to common descent. Wells: “Yet animals and plants possess many features that are similar in structure and position but are clearly not derived from a common ancestor with those features. The camera eye of a vertebrate and the camera eye of a squid or octopus are remarkably similar, but no one thinks they were inherited from a common ancestor that possessed a camera eye.”