Yes. I think that there are some closely related species of organisms that cannot be identified with a dichotomous key.
Dichotomous key is used to classify objects or organisms based on its physical characteristics. Because of that limitation, there are species that may be related according to the dichotomous key but are in fact not or its relation is very minimal whereas there are organisms that may seem unrelated based on their physical characteristics but are actually from the same ancestors.
