One mistake that Atticus definitely makes, as I read the novel, is to underestimate the rage of Bob Ewell. I don't have a copy of the novel on hand, but I'm pretty certain that in a chapter after the trial (I think that it's shortly after Bob spits in Atticus' face) that Atticus makes a comment to the effect that Bob Ewell has had his say and that things would quiet back down again. To me, that's an understandable mistake, but a mistake nonetheless. Bob Ewell doesn't simply forgive and forget.
A related mistake (perhaps even the direct cause of Bob Ewell's mad attack on the Finch children) might have been made in Atticus' questioning of Mayella. He leads her in a line of questioning that strongly points to incest in the Ewell family ("What my papa do don't count") but doesn't really strengthen the case for the defense. Why would he "go there," I've always wondered, if there's nothing to be gained?
The near perfect Atticus Finch is, indeed, not without his faults, and this part of his makeup further strengthens his persona and legacy as one of fiction's most identifiable characters. One specific mistake is committed near the end of the novel when the distraught Atticus wrongly assumes that his son, Jem, is the killer of Bob Ewell. Perhaps it is the shock that he must have suffered after learning of the attack on his children that causes him to think so impractically. To the reader, it must have seemed obvious that someone else (no doubt it was Boo Radley) committed the crime, but Atticus was not thinking clearly at the time. It takes the persistent calm and reasonable nature of Sheriff Heck Tate to finally convince Atticus that it is not Jem who had knifed Bob.
1) he underestimated bob ewell. too naive. "he got it all out of his system that morning." aunt alexandra tried to warn him. "he seems to have a permanat running grudge with everyone connected with that case," and even scout and jem express worry. yet he did not take extra precaution, which led to the attack.
2) atticus is said to be free of prejudice, but it is not true. scout identified the flaws of her father and maycomb- "they gave them christmas baskets,relief cheques at the back of its hand." atticus knew that the ewell children suffered from abuse- but he didn't do anything about it. he even treats them like exhibits and showed jem and scout "how the ewells lived." he is no different from those whites who think the ewells "lived among pigs."
3) atticus failed as a parent - he insisted that jem go on trial although he was already traumatized enough from the T.R. trial. too caught up with his moral values. he also fails to empathize this time with boo radley.
4) another mistake as a lawyer- he took the trial personally, when he should have taken it at a professional level. he let him affect it personally.