It definitely seems like more of the blame here should be shouldered by the police and the courts, who, knowing that the system has problems (and hopefully assured that those problems will be resolved in the future) should put less faith in them, and double-check (against filed papers, for example) potentially dubious results.

This is more expensive in terms of people's times, but it's just part of the cost of adopting the new software, and should be treated as such, possibly by billing the software vendor for the additional manpower required to work with the software during the transition.