Actually, the presumption is that public officials exercise their duties in good faith and for the public interest. That can be rebutted however, and once has been, that presumption disappears, e.g. that idiot public official who testified that any problems were the fault of voters who stupidly and short-sightedly insisted that they could vote on election day.
The machines are a priority black box. Hard to rebutt anything that has to do with the machines.
Also hard to rebutt chain of custody documentation, when such documentation has been lost.
Hard to verify signatures, when any scribble is accepted.
I could go on.