The reason we think that fingerprints on a gun might tell us who used that gun to commit a murder is that we think that we understand the natural processes by which the unique patterns in the skin on the human finger might come to appear on another object and, just as importantly, we think that those natural process are unvarying. If we thought that those patterns just appeared randomly on objects or if we thought they appeared by divine fiat, we could not say that fingerprints on murder weapon constituted evidence of anything.
Unfortunately, miracles don't follow natural processes and they do not occur uniformly. We cannot claim that the Shroud of Turin constitutes evidence of the resurrection of Christ because we have no idea what happens when a human being is supernaturally raised from the dead. We have no basis to assert that any particular piece of evidence is more likely the result of a miracle than a natural cause because we have no idea what kind of evidence a miracle is likely to produce.
Christian apologists will claim that this is simply an anti-supernatural presupposition that skeptics bring to the table, but that is not where the problem lies. The problem lies in the logic of the "inference" tool that we use to draw conclusions from evidence. We infer anything from any particular piece of evidence without some knowledge of the way in which particular causes produce such evidence.