Plot hole: After Rex learned that he was not really a DiMera but in fact a Brady, he suddenly became "poor." But a lot of things don't add up. Firstly, after Tony died, there was never a funeral or a will reading shown, but it seems likely that the twins would have been left something. Secondly, Rex graduated from college in the spring of 2003 and is an incredible genius who invented a laser that turns coal into diamonds. So although he might be on his own financially, he should be able to get a pretty good job without much trouble, but there's no indication that he has even tried. But Rex being poor has instead become a significant plot device, because Bonnie does not want him to marry her daughter Mimi as a direct result of it.
Plot hole: Whenever John moved at all towards Marlena during the exorcism on 4/20/04, Father Jansen ordered him back right away. But when Marlena calls for Belle and Belle kneels right in front of her mother, Father Jansen doesn't say anything. The only reason is so that the scene's drama can be increased when Marlena begins to strangle Belle.
Plot hole: On 3/15/05, Jack picks up the phone in his house and calls Jennifer's cell phone. Unfortunately, before he can tell her what's going on, the Jennifer impostor knocks him out and tells Jennifer that it was a wrong number. However, Jennifer's cell phone should have shown her that the call was coming from her own home, which would have been quite suspicious.
Plot hole: On April 1, 2004, Marlena fell over the penthouse balcony and landed directly on Sami. The next week, everybody was talking about how Lucas saved Sami's life by pushing her out of the way of Marlena. But this makes no sense, as the collision couldn't possibly have been any worse than it was. So what exactly does everybody think Lucas did?
Plot hole: When Lucas pretended to be the killer on 12/16/03, he said that he wanted to give Sami a scare after becoming suspicious of her when he followed her to his mother's hotel suite. But if he was following her, then how did he get to the bedroom before Sami to jump out at her? And where did he get the cloak and mask on the spur of the moment?
Plot hole: How can Rex and Cassie be so close in age to Belle? Marlena gave birth to the twins, her surrogate children, while she was held prisoner by Stefano, some time before her return to Salem in 1991. Belle was born in 1993, so she should be several years younger than her supposed half-siblings. Instead, they all started college together and turned 18 (a huge continuity issue in and of itself) in 2002-2003.
Plot hole: During the week of 9/6/04, Patrick delivered Jennifer's baby, and wrapped the infant in his own red shirt. Eventually, the baby was wrapped in a receiving blanket, and Patrick was wearing the red shirt again. But a newborn baby had been swaddled in that shirt, meaning that it should have been revoltingly unwearable.
Plot hole: After Doug was murdered, Belle told Shawn that Marlena could not have done it because she was with her at the time, which is a lie. Shawn believes her, though, thus quelling his suspicions that Marlena could be the killer. But there's one small problem. Shawn was with Belle on the balcony on 3/5/03 when he received his father's emergency page, leading him to call Bo and learn that his grandfather had been murdered. So there's no way Belle could claim to have been with her mother when the murder occurred; Shawn was with Belle himself.
Plot hole: On 4/5/05, Rex surprises Mimi on the roof with a romantic dinner. He also plays Jesse McCartney's "Beautiful Soul," which Mimi identifies as "their song." But Rex and Mimi started to get together as a couple about two full years ago. Why would "their song" be something that was released in the last two months?
Plot hole: On 1/25/05, Belle asks the jewelry store proprietor to recommend a medal to give to Philip, who is going to war. The lady suggests that Belle buy the same medal she had given her own grandson when he went to war. But on 1/26/05, when Belle gave the medal to Philip, she told him that it was the same as the medal that her grandmother had given to her grandfather when he went off to fight in WWII. If Belle knew about a medal that her grandparents had once exchanged, why didn't she just ask the lady for that particular medal?
Plot hole: On the 11/17/03 episode, it was stated that the sudden darkness on 11/14/03 was the result of an eclipse. But that doesn't make sense at all. The characters were very surprised by the event. However, the times and locations of eclipses are always well known to astronomers. When one is going to happen, close to everyone in the affected area is aware of it. If an eclipse really happened "out of the blue" without anyone expecting it, it would be instantaneously newsworthy on a global level. The explanation that because of the serial killer being featured in all the headlines that they had not noticed the information about the eclipse makes no sense, as the same people who normally know about impending eclipses would have known about this one.
Plot hole: On 7/7/05, Lucas told Sami that Will had called him from summer camp to say he was having a good time but misses Sami. However, just a few episodes earlier, when it was already the same day, Sami was making an American flag dessert that she said was for Lucas and Will. So why wasn't Sami surprised to hear that Will is away from home?
Plot hole: On 12/16/03, Roman and Kate find out that Sami tried to frame Kate for the recent murders, and Kate asks Roman if the fact that Sami would frame her for murder might suggest that she could also be capable of actually committing murder. There are two very strange things about these scenes. The first is that Sami never brings up the fact that Kate framed her for murder years ago, which actually put Sami on death row in 1999. The second is that Sami's attempt to frame Kate seems to be the closest thing to murder Kate can think of to incriminate Sami, even though Sami actually shot a man (in the testicles, no less) in 1994.
Plot hole: In 1998, Billie gave birth to a baby, Georgia, that she believed to be stillborn. When she and Bo found out in 2004 that Georgia was really alive, Billie lamented having missed fifteen years of her daughter's life, and they talked about how their daughter would now be a teenager. But Georgia should only be six years old.
Plot hole: When Zack Brady was hit by a car and severely injured in January of 2006, Dr. Lexie Carver urged Bo and Hope to take him off of life support as Zack had no chance of recovery. To encourage them towards this decision, she pointed out that Zack's liver might be a match for Claire Kiriakis, a baby who was dying of liver failure. However, Lexie failed to mention that liver transplants can be done from live donors because the liver regenerates. Dr. Carver would certainly have known that.
Plot hole: On 7/16/04, Mimi heard on the radio that her brother Patrick was dead, and then she went to Alice's and told her mother Bonnie. But the news never releases the names of victims of any type of fatal event before the family has been notified, so Mimi never should have heard news like that on the radio.
Plot hole: The week of 2/23/04, Marlena tried to kill Shawn by stabbing him to death while he slept, but Jan was in the bed instead. By this time, Marlena had killed seven people, several of them by slashing. So she was a skilled and accomplished killer. Yet somehow, when she was done with Jan, Jan was in good enough health to get out of Shawn's apartment, get out of that building, walk to the Kiriakis mansion, and get upstairs to Nicole's bedroom.