Plot hole: The governor refuses to open the door for the prisoners when they have Vera hostage, and you can hear her saying "no" "return to your units" over the radio, which Channing had to overrule. Later on in the show somehow Vera doesn't know the governor refused and has to find out from Channing. But Vera was there next to the radio the whole time. They use normal radios without earpieces so there is no way she didn't hear. (00:38:05)
Plot hole: Will, Jake, and Vera are continuing their lives with the assumption that Joan Ferguson is dead. When the police found a body they suspected it was Ferguson pending a DNA test, as this was relayed to Vera. It wasn't Ferguson, as she's alive. The police never told the three corrections staff whether it was her. Channing got framed for the death because he got framed for the escape and burial when Jake and Will planted the shovels in his car. His lawyers should have got disclosure.