Continuity mistake: Where Swazye and Moore are at the pottery wheel, seconds after their hands and arms had been smeared with clay, they're clean.
Suggested correction: The director explained this in the commentary. The scene where they are clean isn't meant to be immediately after the clay pot scene. It was just the same evening.
Plot hole: When Carl is helping Molly out after Sam dies, he manages to find Sam's address book in a box, which he needs to launder the money at the bank. So why does he need to convince Molly to take a walk outside so Willie can break in the apartment and steal it? Carl knows which box the address book is in, and could have easily stolen it earlier when Molly was not in the apartment.
Suggested correction: Carl couldn't have stolen the address book earlier; it's possible he didn't know where it was, and he had to use the visit as an excuse, or it's possible he knew where it was but was thwarted because Molly wouldn't ever give him a chance to steal it, since she wasn't leaving the apartment. And he couldn't steal it later, because Molly wasn't leaving the apartment. His only chance was to lure Molly away so that Willy could come in and get it.
Since he worked at the bank with Sam, he could, without raising any red flags, simply ask to copy a few numbers from the book. Also, while he was walking with Molly, how did he contact Willie and tell him to go in? They didn't have texting back then. And how did he not know Molly had come back, if she had been walking with him? Other than the obvious, fourth-wall-breaking excuse that he didn't want us to know he was the villain yet.
Other mistake: At the time Sam is shot his soul separates from his body, indicating that he dies, but in the next shot the ambulance is carrying him to the hospital in order to help him.
Suggested correction: If paramedics think there might be a chance to save someone they will continue treatment until a doctor has made the call to stop. Just because the paramedics continued to try to save him doesn't mean he hadn't already died, just that they were not yet willing to give up.
I've seen Emergency Medical Technicians and County Coroners call "dead at the scene" many times, without any attempt to resuscitate. In Sam's case, in this movie, he certainly seems to be dead, just a moment after the gun discharges.