I've always thought that one of the biggest problems with DNA testing is contamination. It's not factored in to the equations, but here's an example of what can go wrong.
If it didn't have such massive potential consequences, it would be funny. How can you prevent contamination? You can't. Just recognise that it can happen and don't believe anyone that says that their testing methods are 100% accuracte.
When I finally get round to writing up my thoughts on DNA, I shall return to this.