When Carl has the knife in Molly's kitchen, it visibly wobbles and is clearly made of rubber. However, if you look closely you can see it is simply shaking, as Carl is beyond terrified at realizing Sam's ghost is real.
Willie Lopez returns home and calls someone--presumably Carl--to tell him he couldn't get Sam's codebook, because Molly came back home. But Molly was only out of the apartment because Carl coaxed her into leaving, and she wasn't gone for very long. So, Carl should know that he wouldn't have had enough time to get the booklet, and he should have known that Molly was coming back home when they parted company.
When Sam and Molly were fooling around with the pottery wheel, they, quite naturally, had clay all over their hands and up to, and even above, their elbows. In the immediately following love scene, however, their hands and arms are squeaky clean.
When the ghost of Orlando enters Oda Mae's body, he speaks to his widow Ortisha as if it's the first time he's seen her with the new hair color but he was standing alongside the séance and fully able to see Ortisha all the while.
When Carl is desperately trying to find the money that is no longer in the account, Sam can be seen sitting in a chair behind him. At one point, Sam pushes against the wall making the chair roll and scaring Carl. In the next scene a blue chair without wheels appears at the same wall that Sam had just pushed off of.
When the Subway Ghost kicks the cigarette vending machine in anger, you can clearly see that the rows of cigarettes were rigged to go straight down and out the chute, which would not occur simply because the glass was broken. Also, there were also many more packs of cigarettes on the ground than could have come out of the machine, and were obviously pre-placed.
After Oda Mae gives away the check, she says goodbye to Sam and we see a group of extras crossing the street. When the angle switches to the other side of the street, we see one of the same extras (African American lady, box cut hair) crossing the street again.
We are told that Willie Lopez lives in Prospect Place. But when we see him go home when Sam follows, he gets off the J train in Bushwick. Also there is no J train at Franklin St in downtown Manhattan. You would have to take the 1 train.
Willy Lopez apparently has no connection to the drug dealers Carl is working with, since Carl has to explain who they are and what will happen if he doesn't get his job done. Lopez also has no police record. How then does someone like Carl; a wealthy banker; find someone like Willy; a criminal in a low-rent part of town; to steal a code book from Sam?
In the exchange between Molly and Lyle the bank officer, she asks him if that was Oda Mae, and wanted to know what business they had just done. Lyle tells Molly her name (Rita Miller) and said that she was closing an account. By federal law, bank personnel can never discuss the details of one customer's transaction or identity with another. However, Lyle is a "social moron," very likely to have forgotten or not cared enough about the law to keep himself from discussing it with Molly, or intently believing that, because Sam was a bank employee, he could freely discuss it with Molly without fear.
There are a number of inconsistencies concerning Sam touching things when his hands should have gone through. For example, when Sam is in the hospital after his murder he gets out of the chair by grabbing hold of the arm-rests to push himself up out of the chair. However, these could be explained that those things he is trying to intentionally manipulate require concentration, but things that he's used to doing or doing without thought don't require concentration at all as they are instinctively easy.
When Willie is fighting with Sam just prior to shooting him you can see that the gun Willie is using (Walther PPK or similar clone) is in the safe position (i.e. manual safety/decocker is vertical rather than horizontal). Such a gun should not fire.