I think that your point is a little pedantic.
To set it in context before somebody tries to make it much more than it is:
First, confused phylogenetic information is hardly the worst case for evolution, even if it were general (and if it was general I think we would have a rather different version of evolutionary theory).
Second, given that this confusion only gives one group of species it has relatively little weight compared with the overall pattern anyway.
Now if the genetic data showed a pattern inconsistent with evolution altogether then things would be very different.
As it is, I think we can say that there are things that can confuse genetic phylogenies, such as horizontal transfer, hybridisation and rapid radiations. But only the first could even conceivably pose a threat to evolution - and then only if the rate required to explain the genetic data was well above reasonable expectations (and to the best of my knowledge it is not)