LJ sends Quinn down the well, breaking the cover. Later, when Agent Kellerman and his partner show up, they put the "intact" cover back.
When Quinn is first knocked down in the well his cell phone is seen lying open beside him. When he is next shown regaining consciousness he takes the phone out of his pocket to call Kellerman to rescue him. It's highly unlikely that he would have put it back in his pocket before using it. When he is shown in the well upon Kellerman's appearance, he says the battery is dead and both he and the phone are in the exact same position as the first shot after LJ knocks him down the well, indicating the directors simply used the same shot twice.
Quinn has scratches on the right side of his face. After chasing LJ through the woods, the scratches are on the other side in a close-up before once again returning to the right.
When Michael leans over at the start of the episode, there is no tattoo visible on his back
The FBI still has an open case on the DB Cooper hijacking. They have a list they have distributed for four decades now of every serial number on every one of the bills that were part of the ransom. In 1980 a kid digging along a river in the area of the jump found around $5000 of those original bills. Except for this there has never been another bill surface from the hijacking and if one ever did the FBI would be tracing it back to its source. Anyone attempting to spend a significant portion of the bills would bring an enormous amount of heat straight down onto them. If you're a fugitive that just escaped from a max security facility then this would be most unwise.
The DB Cooper character shows Michael the $100 with the serial number to prove he was the "real" DB Cooper. The real DB Cooper extorted only $200,000 in ransom and all in $20 bills.
Charles Westmoreland insinuates he is the real, D.B Cooper after showing Scofield a $100 bill from the heist. Westmoreland's age is revealed to be 59 in 2005 from newspaper clippings in Scofield's apartment. That would mean he would have committed the D.B Cooper heist at around age 25 in 1971. However, the real-life DB cooper was significantly older at the time of the heist, identified as being in his mid forties.