Pence may well be nefariously involved with the take down of Flynn.

“Obama had fired General Flynn as head of the Defense Intelligence Agency, and subsequently told President elect Donald Trump not to hire him. Knowing this, I’m surprised President Trump didn’t reject a resignation from General Flynn and fight to keep him on staff.

Barack Obama and the corrupt Department of Justice wanted the General eliminated from the Trump administration. Why? Because General Michael T. Flynn spent 33 years as an intelligence officer, and he knew the corruption in the Obama administration and the DOJ. They were scared of him, and as such he had to be destroyed. Establishment insiders like Pence, Priebus and others likely helped to accomplish their goal.”

https://newswithviews.com/the-fbi-collusion-to-destroy-general-michael-t-flynn/

A slightly nicer spin on it is that Flynn had no-win choices: Contradict Pence or take the fall himself. https://theconservativetreehouse.com/2018/12/05/occams-razor-michael-flynn/