The tip off was early on when Pence told Trump that Gen. Flynn “lied” to him and recommended that Trump fire him. I always thought that Pence was working with the FBI/CIA.
After reading the details of the whole Flynn charade I wondered if Pence was simply playing the role of the bad guy, and having the “Flynn lied to Pence” story put out there as the reason Flynn was fired — when he was really being fired for other reasons.