Good question. This problem affects multiple steps of a NGS-based forensics product: sample collection, DNA extraction, library preparation, the sequencing itself, alignment/assembly, and statistical variant interpretation all have potential for large biases/error modes that could affect the specificity of these types of methods.
Separately, and outside the forensics realm, there's a trend towards increased regulation of DNA sequencing. For example, NIST has developed/is developing methods to evaluate sequencing platforms: http://www.nist.gov/mml/bbd/dna-022514.cfm. This is relevant to other sequencing applications too (e.g. personalized medicine, somatic tumor profiling, etc). The FDA are also involved here, but more focused on medical applications.
So, I think collectively through both the increase in the forensics community regulating forensics NGS applications, and more broadly the biomedical science/technology community regulating general NGS platforms, we'll see good technology validation standards (at least in the U.S.). But the significantly higher complexity of these systems does introduce more opportunity for error, so it's entirely possible we'll see similar biases in NGS based forensics.
One specific answer is that the FBI is gearing up to regulate new devices in this area (https://www.fbi.gov/about-us/lab/biometric-analysis/codis/st...). For example, in this publication (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757157/), they specifically analyze an IonTorrent PGM for use in forensics applications, which we'll probably see them do for various other platforms that come on to the market.
Separately, and outside the forensics realm, there's a trend towards increased regulation of DNA sequencing. For example, NIST has developed/is developing methods to evaluate sequencing platforms: http://www.nist.gov/mml/bbd/dna-022514.cfm. This is relevant to other sequencing applications too (e.g. personalized medicine, somatic tumor profiling, etc). The FDA are also involved here, but more focused on medical applications.
So, I think collectively through both the increase in the forensics community regulating forensics NGS applications, and more broadly the biomedical science/technology community regulating general NGS platforms, we'll see good technology validation standards (at least in the U.S.). But the significantly higher complexity of these systems does introduce more opportunity for error, so it's entirely possible we'll see similar biases in NGS based forensics.