There are some inconsistencies in both of their testimonies. Bob Ewell testified that he witnessed Mayella having sexual intercourse with Tom from the window outside the house. Mayella testified that her father had run inside the house and asked her "who done it?" So, why would he have had to ask her if he had seen "who done it?"
Mayella testified that Tom choked her, but Bob Ewell's testimony said that she was beat up in the face, and her eye was blackened. Mayella did not even mention getting beat up in the face until Atticus brought it up, and then she seemed confused.
"It's an easy question, Miss Mayella, so I'll try again. Do you remember him beating you about the face?" Atticus's voice had lost its comfortableness; he was speaking in his arid, detached professional voice. "Do you remember him beating you about the face?"
"No, I don't recollect if he hit me. I mean yes I do, he hit me."
"Was your last sentence your answer?"
"Huh? Yes, he hit-I just don't remember, I just don't remember . . . it all happened so quick.”
Mayella seemed more confused than her father about what really happened. She was much more flustered than he, probably because he was used to lying more than she and his lies came more readily. Mayella was much more nervous than her father when she testified not only because of her age but because she no doubt feared her father would beat her up even further if she made any mistakes. Atticus took advantage of this in his questioning of Mayella, which was much longer than his questioning of Bob Ewell.
Read about it here on enotes.
Significantly, Mayella's testimony differs from her father's. For one thing, in Chapter 18, she testifies that Tom Robinson choked her as she faced him, then he "took advantage of her." She says nothing about having been struck in the right eye (or the left, for that matter) as her father, Tom Ewell, has done previously in Chapter 17. And, when Atticus questions her, "Do you remember his beating you about the face?" Mayella hesitates. When Atticus reminds her that she seems certain about the choking, and asks her again about being hit, she replies,
'No, I don't recollect if he hit me. I mean yes I do, he hit me.'
'Was your last sentence your answer?' [Atticus]
'Huh? yes, he hit--I just don't remember, I just don't remember....it all happened so quick.'
Unlike Mayella, Tom Ewell has been absolutely affirmative about Mayella's eye having been blackened. He also has said nothing about Mayella's neck being bruised, red, etc. which would have indicated choking, whereas she has repeatedly testified to this action.
Obviously, there is a question of credibility with the witnesses. In addition, Mayella is vague about when her father arrived on the scene,
I don't remember too good, but next thing I knew Papa was in the room a'standin' over me hollerin' who done it, who done it?"
whereas Mr. Ewell has stated that he looked through the window and saw Tom Robinson on top of his daughter. Contrary to this is Mayella's citing her father's having asked "Who done it, who done it?"
These discrepancies between the father's and the daughter's testimonies, along with the fact that Mayella possesses a right black eye which indicates that a left-handed person must have hit her (her father is left-handed and Tom's left arm is useless) are what Atticus Finch believes will prove the innocence of his defendant.
Also, with one of the main themes of Lee's novel as that of Prejudice, the description of the hearings of Tom Robinson's trial, in conjunction with the verdict of the jury, clearly demonstrates such prejudice. Indeed, the testimony of Bob Ewell and of Mayella are pivotal to the development of the theme of Prejudice, a development that becomes apparent after a close reading.
In my opinion, there really is not any significant difference between their testimonies. Mr. Ewell does not testify to anything much so what he says does not really contradict what his daughter says.
What is useful in defending Tom Robinson is the inconsistencies within each person's testimony. Why, for example, didn't Mr. Ewell call a doctor. More importantly, how is it possible that Tom did all those things to Mayella when he cannot use his left hand? How could he hit her right eye? How could he choke her? These would be hard for him with essentially no left hand.