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.