I don't think the thinking error is restricted to atheist but is a problem with Western culture and it is Christianity, not science, that shaped Western culture. Science played a big role in our progress, but not in shaping our cultural heritage that is largely our cultural subconscious. So Christians and atheist know all the answers and all things are only true or false.
To be scientific, when there is a lack of evidence the conclusion is "I don't know". Right now we do not have the evidence to scientifically explain Peter the Roman's experience. I am sure the atheist think they are being scientific but they aren't because they insist they know something without good evidence. Such as labeling Peter the Roman's experience supernatural and we all know the supernatural is false, so Perter the Roman could not have experienced what he believes he experienced.

What is the problem with accepting we do not know somethings? And if we don't get out of this rut, we never will know.