Plot hole: On 12/28/04, Sami and Belle talk about how they used to play with Barbies as kids, and how Sami made Belle promise that she would let Sami get married before her, or else she'd tear the head off of Belle's Barbie doll. But when Belle was born, Sami was already a teenager; Sami actually kidnapped Belle and tried to sell her on the black market. So Sami and Belle were never kids together, and the described interaction is impossible.
Plot hole: On 8/9/04, Patrick told Hope that she would be able to jam the force field by "hitting the keys in an even and then an odd number sequence." This phrase is completely meaningless, but it is all the information that Patrick gave Hope about the keypad, which we had previously seen was a regular nine (or ten) digit keypad. And yet, Hope was able to get back through.
Plot hole: On 1/13/04, Marlena provides what may be the deciding testimony in Tony's hearing. Marlena is introduced to the court as a "criminal psychiatrist," despite never before being credited with that specialty. Her brief statement had nothing to do with psychiatry or the facts of the case, and didn't even provide any insight of the sort that a character witness might. She basically said, "I don't think Tony is the murderer." I don't see how this would have any bearing on the case, or would even be admissible.
Plot hole: On 9/14/04, Hope tells Patrick that Billie Reed is the only person who has ever come between her and Bo. But that statement is more than a little ridiculous. Stefano DiMera, Princess Gina, Megan Hathaway, Larry Welch, and John Black have all come between Bo and Hope.
Plot hole: On 6/8/04, when Marlena first saw Victor on Melaswen, Victor told her all about how Jan tried to murder him under Nicole's orders. Then, in May of 2005, Marlena finally returns to Salem and soon has several civil encounters with Nicole, as if she doesn't know that the woman conspired to commit murder. She also fails to denounce Jan, even though Marlena's daughter's best friend Mimi could greatly benefit from such a revelation since she currently stands accused of attacking the woman.
Plot hole: On 10/6/03, Sami tries to listen at the door when Marlena meets with Kate in the latter's office at Basic Black. She says to herself that she wants to find out Kate's secret. But Sami already knows that Kate was once a prostitute. Sami used evidence of Kate's past to blackmail Kate and Victor; Kate's son Austin found out, and that was one of the reasons why he left Sami at the altar. Even though Sami can't know for sure that this is the same secret that is now in question, she is acting as if she knows nothing incriminating about Kate.
Plot hole: On 12/08/03, Belle and Shawn talk on the phone, and Belle briefly mentions something about how much she's enjoying Paris. But Belle was sent to Milan to keep her safe from the killer, and Jan also said that she had seen Belle while she was in Milan herself. Nobody ever said anything about her going to Paris.
Plot hole: Around 3/14/05, the Jennifer impostor told Jack that it was too late at night to get Abigail from Chelsea's house where she was staying. Jack agreed that it was very late at night, and they also talked about how late it was when the impostor told Jack that the ISA wanted to debrief him right away. Then, later that same night, it was Alice's anniversary party, which wouldn't make sense if it had already been late at night to begin with.
Plot hole: Belle, Philip, and especially Mimi have been concerned about paying the rent on the loft over the course of their living there in various combinations in 2003-2004. However, when Brady first moved in there in 2002, it was stated that his and Belle's father, John Black, owned the loft. So nobody should have to pay rent on it at all.
Plot hole: On 4/16/04 and 4/19/04, John told Marlena that he had an idea that could prove Marlena's innocence, but could also potentially be fatal. Then, on 4/20/04, John acted surprised and upset when he learned that Father Jansen's possession test could have killed Marlena. But John was previously a priest - he even exorcised Marlena when she was possessed in 1995 - and definitely seemed to know that the procedure could be deadly, so his shocked disposition makes no sense.
Plot hole: On 10/8/04, Hope drew a comparison between the current situation and the movie "A Shark's Tale", saying Zach wanted to go as the shark that didn't eat people. But Hope had been trapped on an isolated island for weeks, since well before that movie came out, so how could she know anything about it?
Plot hole: On 11/29/04, Philip and Belle tell Sami that they want to use her wedding date, because they want to get married very soon, before Philip is shipped out. But Lucas later mentions that he and Sami don't even have invitations yet, which would indicate that their intended wedding date isn't very soon at all.
Plot hole: When Marlena finds out that Lucas has been working for Tony DiMera, she is angry and upset. He says it's none of her business, but she says that it is her business because she is the grandmother of Lucas' son, Will. Sami finds out about Lucas' new job about a month later, and is shocked. If Marlena was so concerned about Will, why didn't she say anything about Lucas' new job to Sami, Will's mother?
Plot hole: On 3/9/05, Chelsea's mother told Chelsea and Abby that it was bedtime. Then the girls snuck out to go to the Cheating Heart. Later the same night, Abby, Chelsea, and Jennifer were all at Alice's anniversary party, so it was apparently no longer after bedtime. Then, later still, Jennifer was upset that Abby wasn't at the house and therefore was breaking curfew, even though Abby was staying at Chelsea's house in the first place. Nothing about that timeline makes any sense.
Plot hole: On 10/27/03, Brady picks up a newspaper with the headline, "Suspect List Grows in Police Slaying." But that doesn't make any sense. The page features pictures of the same seven people who have been suspects for the last few weeks, and no other suspects have come to light. The suspect list hasn't grown at all.