Yes, every species WAS perfect, MAN was perfect.In any event, only interpretations have changed due to a changes in the moral of society. The bible still very much supports such actions of discrimination. And yes, the contradictions are present especially you take the meaning literally.
Moving on, I have recently been considering creation ideas vs what we can observe and call evolution. Now, we can obviously see species adapt and change. Most creationists would however say that it is still the same species and to some point, I would agree. However, did the bible not say that god made every individual organism and every species is perfect? What reason is there for a species to change if it is supposed to be perfect?
Read genesis