The idea that all organisms should be perfectly designed (argument from natural evil) is one commonly used against the idea of creation. However, while this might be true for a pre-fall creation, it is not true for a post-fall creation. There is indeed degradation that has occurred from the fall.
Some sections of DNA are corrupted copies of functional coding DNA, but mutations in them, such as stop codons early in the sequence, show that they cannot have retained the same function as the coding copy.
The idea that they are corrupted is an assumption. They are obviously not the same, but the reasons why are not necessarily known. These could at one point have been active, but been deactivated by a control mechanism. They could also be used to verify the integrity of the original. The fact that biologists have not found a use for these does not mean that they are non-functional. Our knowledge of biochemistry, while great, is still in its infancy.
http://creationwiki.org/"Junk"_DNA_is_not_really_junk_(Talk.Origins)