What was some of the evidence that proved that Bob Ewell was right about who raped Mayella. What could prove the prosecutor's argument that Tom Robinson did rape Mayella was true?
By posing this very question, you are reading the novel "against the grain" or are reading as what is called a "resisting reader," which can be a very good and challenging way to read. I'm not sure that it is possible to marshall solid evidence that Tom Robinson indeed raped Mayella, but it is possible, as your question asks us to do, to resist the novel's promptings and to challenge the standard reading of the novel that Mayella is wholly guilty and Tom is wholly innocent.
(I would recommend that someone begin to read the novel "against the grain" only after they are certain that they have fully understood the standard reading and want to take things one step further. This strategy is a way to attempt to raise and answer questions that are not normally asked, but it's not the place to start when we first pick up a novel.)
We might begin by arguing that the novel is not an objective account of anything; if it were an objective account, how would we make sense of the opening, strongly nostalgic statements about how "it was hotter then" and "people moved slowly then"? Rather than offering an objective account, the novel instills in the reader certain biases and steers the reader toward certain conclusions. We are supposed to like (and to believe) the Finches, for example, and we are not supposed to like (or to believe) the Ewells. In reviewing the novel with this bias in mind, you are certain to find mutliple instances (the "evidence") of how the reader is not given a neutral account of the whole event.
Of course, we might then have to acknowledge that in the American court of law, the burden of proof is on the accuser and -- at least in the account that we are given -- that the accuser did not deliver that proof in court.
In the end, then, we might not be able to convince anyone that Tom Robinson indeed raped Mayella, but we might be able to cast some doubt on the standard reading of the novel. Like the jury, which quickly handed out a guilty verdict although there was inadequate evidence, the standard reading of To Kill a Mockingbird may arrive prematurely at a conclusion -- a certainty in Tom Robinson's innocence (which is much more than the legal pronouncement of "not guilty") -- that itself remains open to questions.
I assume you are taking a stance that Tom Robinson actually did rape Mayella Ewell (which goes against Scout's narrative that suggests the Ewells made up the story). This will be tough to prove, since the only evidence comes from (1) the mouths of Bob and Mayella Ewell, which contradict the testimony of Tom, who claims he didn't touch her; and (2) the bruises on Mayella's neck and face. Sheriff Heck Tate took Bob Ewell's word as fact, and no doctor was ever called nor was Mayella ever checked for any kind of vaginal trauma (no modern rape kit was available during the 1930s). Tom admitted to being in Mayella's house, but the evidence all boils down to the Ewells' word against that of Tom's.
The only "evidence" that Tom raped Mayella are the witness accounts, which aren't credible anyway. Those who know, and are willing to face, the facts know that Tom did not rape Mayella. However, many people are only willing to see that a white woman is accusing a black man, and that is enough for them. These circumstances are what make Atticus's plight that much more important and that much more difficult. He knows the facts and tries his best to defend Tom, even though he knows the odds are stacked against him.
As the previous post notes, there is no substantial evidence that Tom Robinson has done anything wrong. Circumstantial evidence puts Tom inside the house of the Ewells--why would he be there? the prosecutor implies--and he has been seen by Mayella's father--and Bob Ewell implies that he was "rutting on her."
No credible evidence in the novel supports the claim that Tom raped Mayella. It is simply her word against his. Unfortunately, because he is black and she is white, his word is given little credence by the jury, even though Atticus makes a compelling case that Tom did not rape Mayella.
In fact the point was toward Bob Ewell hurting his daughter because Mayella was hit on the right side of her face and the only person who was left handed was her father. This meant that he was the cause of her bruises. If Tom was guilty, then the only evidence we have against him is what Mayella and her father would say.
Atticus asks Bob Ewell to write out his name on a piece of paper. He and the judge observed that he is left-handed. Since Tom Robinson's left hand is useless (It got caught in a cotton gin when he was a young boy) and Bob Ewell is drunk most of the time, this proves that Bob Ewell raped her, with her face being bruised on the right side of her face. Bob Ewell raped Mayella because he caught Tom Robinson and her kissing.