I don't see how this causes even the slightest problem. The fact is that early classification methodology was based mostly on anatomical features. This has been superseded by classification based on genetics because it is more specific. Evolution should not be seen as a process having any particular direction. Early classifications grouped whales with fish. The genetic information now revealed simply gives us more information and allows correction of previous misconceptions. That’s the benefit of the scientific process - it is self correcting. Nothing is proven, only disproven. It doesn’t start out with the answer and then ignore or deny the evidence.