Plot hole: When both Gwen and Eve were in prison in January of 2005, Ethan was trying to get Theresa (whom Gwen had stabbed in the back) to drop the charge of attempted murder so that Gwen would be able to leave the prison. At the same time, Eve was being charged with three attempted murders, including that of Julian in 2001. But Julian loves Eve, and they have reconciled any differences they had three years ago, so why doesn't he also have the option to drop one charge of attempted murder?
Plot hole: During the party where it was revealed that Ethan is not a Crane and Theresa knew he wasn't, Gwen accidentally reveals she also knew. Even though he is upset with Theresa for keeping it a secret, Ethan says he can forgive her because he thinks she kept it a secret to protect him and that she never would have revealed the information to the tabloid. But Gwen says 'then why did she save the document on her lap top?' How did Gwen know the information was on Theresa's lap top? When she says that, it reveals that not only did she know that Ethan was not a Crane but that she knew Theresa knew, and that she was probably the one that sent the info to the tabloid.
Continuity mistake: The morning after the tsunamis, Little Ethan was at Pilar's house. He came running out of his bedroom and accidentally saw Rachel's corpse. Later, Ethan Winthrop and Gwen came to the house, but left alone. Theresa later left the house, and then Alistair brought her into the Crane mansion with much fanfare. She entered alone, and then went up to see Jane, still alone. But when we next saw her, she was in Jane's bedroom with Little Ethan, even though Little Ethan never left Pilar's house.
Factual error: Dr. Eve Russell seems to be a "jack of all trades" in the medical profession, but it's impossible for her to know everything about every medical condition. When Theresa is going to marry Ethan, she goes and gets birth control pills and takes her first pill the day before the wedding. That night they make love. The next day, the wedding never takes place and Theresa flies off to find Julian. She forgets her second pill and sleeps with Julian. Eve tells her that since she didn't take a pill before sleeping with Julian then the baby is his. Any doctor would know that (and also suggest that) birth control pills are not completely effective until a person has been taking them for at least seven days, and a secondary form of birth control should be used. There's no way that Theresa's just taking 1 pill would protect her from being pregnant by Ethan, and this would still warrant a paternity test.
Plot hole: On 9/27/04, Martin went to Sheridan's cottage and retrieved a gun that he said he had hidden there many years earlier, when the Lopez-Fitzgerald family lived there. But Beth burned Sheridan's cottage down in March of 2003, and it was completely rebuilt. So Martin's gun would not have been there anymore.
Plot hole: On 12/24/04, Beth was able to identify Mrs. Wheeler as Katherine Crane because of the heart-shaped birthmark on the back of her neck. Given that Katherine had extensive plastic surgery to hide her identity before she left Harmony, to the point that she is completely unrecognizable from facial features, why on earth would she leave such a distinctive marking untouched?
Plot hole: Charity's promises don't seem to carry much weight. In the summer of 2001, the talking tree told her that Miguel would drown in the river unless she gave him up, and she agreed. They stayed together, though, and were even engaged to be married in December of 2002. The engagement fell through when Kay turned out to be pregnant with Miguel's baby, but they got back together again the next year. Then, in the summer of 2003, Death offered Charity a way to save Kay's baby, Maria, who was near death. He would spare the child if Charity agreed to give up Miguel. So she agreed. And as of December, 2003, they are still together. It's like these promises just never happened.
Plot hole: In December, 2003, Theresa is fighting the Cranes for custody of her son, Little Ethan. Fox and Whitney overhear that Julian and Rebecca are paying off Judge Reilly to rule in favor of them at every turn. Fox and Whitney share the information with Ethan and Theresa, who tell Theresa's lawyer Woody. When Rebecca discovers that Ethan is secretly helping Theresa, and he has to stop, Woody says that the case is hopeless unless they can turn the tide of public opinion against the Cranes. But why does nobody think of exposing Judge Reilly's corruption, so that the case can continue on a fair playing field, where Theresa is sure to win?
Plot hole: Throughout the week of 5/31/04, Antonio and Hank looked for Sheridan and Luis. Antonio repeatedly stated to Hank, in no uncertain terms, his intention to kill Luis. This was no idle threat; Antonio freely displayed the gun he had, and he had previously shot at Luis. Hank is a police officer, and a much closer friend to Luis than to Antonio. So why doesn't he arrest Antonio for attempted murder?
Plot hole: On 7/21/04, Tabitha was using night vision binoculars to spy on Charity and Ivy, and she lamented that they did not enable her to hear their conversation. If she wants to hear them, then why doesn't she use her scrying bowl? It lets her see and hear conversations taking place anywhere in Harmony, and she has been consistently able to use it even without her full powers.
Plot hole: In December 2003, Rebecca and Julian are planning their wedding. Rebecca is blackmailing Julian into marrying her. Except, aren't they already married? Julian had his accidental marriage to Theresa annulled, and immediately married Rebecca (offscreen). Then it was revealed that Julian and Theresa had actually slept together, which nullified the annullment and Julian's marriage to Rebecca. But then it was further revealed the Julian and Theresa had never been married at all, which should have reinstated Julian's marriage to Rebecca. Instead, the previous wedding was never referenced.
Factual error: On 4/5/07, Chad had a flashback to when he met Vincent at a gay bar, over a year earlier. The song playing in the bar was Pink's "U + Ur Hand," which came from a CD that wasn't released until months after the scene took place. That particular song wasn't released as a single until about an additional year later.
Plot hole: On 10/4/04, Paloma received a call on her cell phone from her Aunt Maria. But earlier in the year, the only way that Paloma and other people in Puerta Arena could communicate with people in Harmony was via a very low quality telephone land line. And even if one of the Cranes had given Paloma a cell phone when she arrived in Harmony, how would her Aunt Maria have the number?
Continuity mistake: On 6/24/04, Fox told Whitney that the kitchen at the Sea Cliff Inn had closed for the night. He managed to convince the cook to make a couple of hamburgers for him and Whitney. (This happened offscreen, but they talked about it before and after.) Later that same night, on 7/6/04, Fox and Whitney went with Theresa and Chad to have a full dinner at the hotel's restaurant, hours after the kitchen had supposedly closed for the night.
Other mistake: In the summer of 2004, in Puerto Arena, Paloma met a man, Nick, who told her that Luis and the other Lopez-Fitzgeralds were just trying to use her, and didn't really love her. Later that night, Nick kidnapped Paloma and tried to rape and murder her. She stopped him by bludgeoning him with a rock, and later throwing him into a support pillar that resulted in a structure collapsing on him and presumably killing him, before reuniting with Luis, Sheridan, and the Wheelers. And yet that fall, after she had returned to Harmony, Paloma flashed back to what Nick had told her and behaved as if she believed what the murdering rapist had told her about the people who ultimately rescued her from him.