The presumption becomes problematic mostly when the operator of the computer is the same party who is being persecuted. 1) It is difficult or impossible for any outsider to inspect the workings of the computer, 2) the operator has every incentive to fake the outputs of the computer or hide the errors.

Related issue, but from the opposite perspective: some years ago I remember the copyright trolls using their own logs of the bittorrent swarm as an evidence in courts. Faking of this data would have been both very easy and pretty much impossible to detect by an outsider. Also they had a massive financial incentive to do so. The fact that this "evidence" was considered in the courts seemed outrageous to me.