Plot hole: They found seminal fluid left in Caroline Polhemus. Why didn't they subject it to DNA testing, which would have been a powerful indicator of Sabich's guilt? Fertility (or otherwise) has nothing to do with it - as well as non-motile sperm (which contain DNA anyway) the seminal fluid would contain discarded skin and blood calls in abundance. DNA testing was first used in a criminal case in 1985 and was in fairly common use by 1988.
Plot hole: At the end of the film, we see Edward carving ice sculptures in his mansion. How did he get the ice up there? First of all, it takes place in a warm climate and I didn't see a freezer up there in the castle. He couldn't have gotten ice from town because firstly he had scissors for hands and couldn't have gripped the ice. And, even if by some miracle he could, he wouldn't be able to buy any from town because everyone in town but Kim was convinced that Edward was dead, she told everyone that they killed each other. And Kim didn't bring it to him because she told her granddaughter in the end that she never saw him again after that night. So where did he get that ice?
Plot hole: Peyton had his face burned in the explosion. In fact, he basically lost his lips, so he should not be able to talk very easily. While he could probably learn to speak normally again through other movements with his mouth and tongue, he does so too quickly to make logical sense. And his uncanny ability to almost perfectly mimic his enemies could probably be learned over time, but again is too quick to make sense.
Plot hole: Detective Mason Storm has been in a coma for a number of years, so how is it that on the day he awakens from the coma, he not only has the strength to move his bed down corridors, but also knows the layout of the hospital?
Plot hole: Cindy manages to pick Crisp out of a line-up even though she was hidden in a box and didn't see him, she only heard his voice. But even with that, he isn't asked to speak during the line-up.
Plot hole: When Carmine tells Clark about the job he wants him to do, he tells Clark to deliver a package for a "Larry London." Once at Larry's home, they are greeted by Edward, who lives with Larry. Clark and Steve introduce themselves and ask if he is Edward, to which Edward replies he is. Only problem is Edward is never mentioned by Carmine or anyone else, so how do Clark and Steve know about Edward? (00:20:00)
Plot hole: Hayes continues his harassment by calling the police and provokes Drake into assaulting him. When the police come and sees Hayes injured, they take Drake away immediately without asking any questions or investigating. No law authorities would ever take away someone with mere assumptions or without investigating, regardless of a history of Drake trying to force Hayes out by shutting off the utilities. Completely unrealistic.
Plot hole: When the clerk is scratching the lottery tickets for the robber, when he scratches the second ticket he only scratches off two out of three numbers on the ticket, but still says it's not a winner.