This is true for all forms of crime. No form of evidence is perfect: eyewitness accounts (human memory is terrible), DNA/fingerprinting/similar (mismatches do occur), circumstantial evidence (obviously not hard proof), confessions (people do dumb things in stressful situations, could be coerced), picture/video (becoming increasingly easy to fake, can be taken out of context).

As a result, when looking at rape cases (like with other crimes), we use degrees of certainty and corroborate multiple sources of evidence. The legal system in the US requires "beyond a reasonable doubt", not "100% certain" - because the latter is impossible.