The ‘bad-design’ objection is from observing the natural data and claiming that it could not have been designed because there are some things that lack proper function or there could have been a better way for a certain [i.e. organ] to function. This objection is often made by many theistic evolutionists, though, still non-theists object as well, is based on an inappropriate and misconceived understanding of design. The design hypothesis merely states that there is intelligent causation that permits the existence of life (a probability factor). Optimality of what has been designed is not a criterion for design. Motor vehicles break down and computers crash. With comparing motor vehicles to design, there is a natural decay and effects of heat, friction, and weather decay. What is interesting about the comparison to malfunctioning software is that a frequently known cause of malfunction is an intentionally designed malware or virus, which has been designed for the primary purpose of malfunction, it is designed to break down or decompose a previous design. Where this analogy fits with the argument, primarily in the claim of vestigial organs or other less-than-optimal structures, is that that the appearance of other bacteria, disease, or even cancer could be the case that such were designed for a purpose of breaking down other design components.
 The theistic objection from bad design, most notably made by Francisco Ayala, is usually coupled with the problem of evil objection.
 I understand this analogy and point invites the problem of evil to wreak havoc on the argument. I personally deny the existence of so-called “natural evil.” Cancer, disease, infection, certain bacteria, etc., are either designed with that function and are mislabeled as “bad.” It may also be the case that mutations have changed living organisms from their initial functions (a claim entirely consistent with the design hypothesis).