I don't know of any FBI-specific issues with DNA work; but various crime labs have had issues with atrociously sloppy practices that tend to go unchallenged, or overtly hidden, for some years. The big FBI story is definitely the "yeah, we basically didn't do a single hair analysis right for two decades; also hair analysis in general is probably bullshit" issue.
In general, DNA-based techniques have the advantage that they are actually 'science', as originally developed by scientists looking for useful research tools and facing some possibility of falsification, embarassing retractions, etc. It requires some skill, and considerable attention to good standards of cleanliness, bench technique, etc.(especially if PCR is involved; that technique is practically black magic it's so good at picking up otherwise impossible to detect DNA; but it is equally good at amplifying your accidental contamination of the sample by a few orders of magnitude)
Much of the rest of forensic 'science', is little better than polygraphs and phrenology. 'Bite mark analysis', in particular, is a tragicomedy.