The scientific evidence does not favor evolution but that doesn't mean we know all the answers. In fact some people who agree evolution is unlikely, nonetheless argue for common descent. This can be confusing because common descent is so often presented as integral to Darwin's idea. But this need not be the case.
Evolutionary thought entertains a seemingly unbounded spectrum of hypotheses about how the species arose. It is by no means limited to natural selection, or even common descent. At the core of evolutionary thought is naturalism. The origin of species must be explained naturalistically. Beyond that, practically anything is allowed.
Common descent can also be an open-ended idea. Yes, it is usually considered to be within evolution's strictly naturalistic paradigm, but that is not a necessary constraint. For many people, it is clear that naturalistic explanations don't do a very good job, but nonetheless there is evidence for shared ancestry.
What all this means is that when one person argues against common descent and another for common descent, they may actually be not too far apart. Hopefully we all acknowledge the broad outlines of the evidence. And hopefully we all understand the important role of metaphysics in interpreting that evidence.
But such shared understandings do not narrow us to a single choice. Some may favor common descent while others may not. That does not mean the former denies the evidence against common descent, or that the latter denies the evidence for it. It simply means that our current level of knowledge leaves us with a substantially underdetermined origins problem. We simply do not have sufficient knowledge or evidence, evolutionists notwithstanding, to make heavy-handed declarations about what must be accepted as fact.
The knowledgeable person arguing for common descent views its evidential problems as reasons to reject marrying common descent to evolution, but not rejecting the concept of common descent altogether. But this person's view of common descent is different from the usual evolutionary view, which typically restricts common descent to be within the strictly naturalistic paradigm.
Clearly, it is crucial for people to establish unambiguous definitions for how they are viewing common descent. Most importantly, is their version restricted to naturalism, or not? For instance, those arguing against common descent may have the strict naturalism of evolution in view. In that case, they are not opposing those who, for instance, argue for common descent from an intelligent design perspective.
In my view, evolutionary thought has badly failed on today's science. And so with it the strictly naturalistic version of common descent likewise thus far fails. The only reason to think otherwise is if one carries a priori metaphysical prejudices, as evolutionists do, which color the interpretation of the evidence.
But given this correct understanding of today's science, the question of a broader version of common descent becomes, in my view, far more underdetermined and far more difficult to assess. Problems that are not amenable to methodological naturalism are above my paygrade.