Plot hole: At the beginning of the movie, Reese (and Walker) rob from a "drop" at Alcatraz. Reese uses that money to pay off "The Organization." At the end of the movie Brewster tells Walker the only place to get cash is at the drop. "The drop is the same but the location has changed." Brewster receives the money at the drop. This makes it clear the original drop was stealing from "The Organization." Why would Reese be able to pay off "The Organization" by stealing their own money from them?
Plot hole: The neighbor girl, using a pre-arranged code, rings Audrey Hepburn's apartment twice when Richard Crenna leaves the phone booth across the street. Hepburn thinks she now knows that Crenna is mixed up with Alan Arkin's strange mix of strange friends who have come to get back the long missing heroin-filled doll. However, anybody could have been coming out of the phone booth. It strains logic that Suzy would make that deduction. (01:25:00 - 01:31:00)