There are a number of possible answers. The question of what kind of designer makes a number of different species with the same damaged gene, assumes that the gene sequence has no function, which as I've tried to say, is unknown at the present time, and which is a claim that assumes full knowledge of the organisms history. How can one be certain that an apparently functionless structure is really functionless? It may be that we lack the knowledge necessary to appreciate its function. Alternatively, if the gene really is a psuedogene, it still says nothing about about whether it descended from a universal common ancestor, or not. It could have just as easily descended from one of many independently created organisms which had the same propensity for as a yet unknown reason for this defect.
Why is the gene there at all? I don't know. That's like asking how you get anything as fantastic as genes in the first place. Why must God fulfill my expectations of universal, optimal engineering design? Or, how do I know that these defective genes are not remmants of some earlier optimal Design that has been damaged? Why do some primates have the ability to synthesize ascorbic acid and some birds, bats and fish don't? Why doesn't the fact the some species can and some can't mitigate against the hypothesis of universal common descent? Darwinian explanation of common ancestry does not really depend on this line of evidence because it can accommodative either the evidence or the lack of it. It is therefore not, imho, conclusive proof of universal common descent.
Cordially,