Plot hole: In the bait and switch section, why does anyone involved agree to Leland being Ben's attorney when both victims are relatives of Leland? Neither Ben nor any of the police are in on Cooper's plan, and it seems implausible at best that they would agree to this.
Plot hole: In the season 1 finale, after they have brought James into the the station Cooper hands Truman a note and asked if he would investigate this. A few minutes later Truman comes back in with the coke that Bobby planted in James' gas tank. Cooper then asks James why he had coke in his gas tank. Cooper shouldn't know where the coke was found, Bobby never mentioned to Lucy where he put it and Truman never told Cooper where he found it.