Plot hole: On 7/8/04, Belle listened to her answering machine messages, hoping that Shawn may have called her. Her outgoing message was, "This is Belle. You know what to do. If this is Shawn, please call me." That doesn't make any sense. If Shawn is hearing that message, then he has indeed called her and doesn't need to be told to do so. And if he doesn't call, he will never hear the message asking him to call.
Plot hole: In January of 2005, John became a drug addict and was confronted by Nicole, Brady, and Kate. However, John was exhibiting all of the characteristic behaviors of drug addiction (lying, stealing, denying the need for help) as well as total chemical dependence, later on the same day that he first stole and injected painkillers. No addiction could progress that quickly.
Plot hole: New Salem is supposed to be in the Caribbean, while actual Salem is in the Midwest (near Chicago). When Hope and Patrick's plane crashed in August of 2004, it was close enough to New Salem that they washed up there. But it was also close enough to Salem that Bo was able to take a helicopter out to the crash site. Helicopters have a maximum range of 500 miles, while the Caribbean is over a thousand miles from the upper Midwest, so this is impossible.
Plot hole: On 9/21/04, when Shawn turned up at the hospital, injured, the first person Dr. Carver called was Belle. Why? She's hardly his next of kin. Shawn's grandfather, Shawn Sr., and his grandmother, Julie, both should have been contacted first.
Plot hole: On 12/29/04, Kate told Belle that "the invitations - they're being rush-printed by a Basic Black printing company," in reference to her wedding invitations. But earlier in the episode, Celeste already had a wedding invitation that a messenger had given to her.
Answer: They haven't mentioned them in a long time. Once they stopped trying to make him look guilty his headaches suddenly disappeared. It may still be explained later as the SK storyline is supposed to not be tied up till early 2005.
Jack's Revenge