My biggest complaint concerned their "statistical" analysis. It was very ad-hoc with very little rigor and the assumptions weren't explained well and they may or may not have been valid. Additionally if you assume for the sake of roundness that there were only 60,000 families, you would expect to see this cluster of names in 100 tombs. So overall it was a very weak argument.
Additionally they linked their ossuaries to the James ossuary, an alleged forgery. The ossuary is real, but the inscription is suposedly a modern addition. It turns out that one of the 10 ossuaries that were found in the Talpiot Tombs went missing. The film claims that the James ossuary is the missing ossuary. Since the inscription is a forgery, it would cast into doubt all of the inscriptions if there is in fact a link between the ossuaries.
Overall the film, while it was about two hours in length, could have been presented in 15 minutes. In fact there wasn't much new information that wasn't contained in their original media circuit on the Today show and others.