Here's the thing with the Flynn fiasco. General Flynn was the National Security Advisor to the President of the United States. People who are read in to National Security issues are authorized to lie, even under oath in a court of law, to protect National Security information.
Flynn did talk about sanctions with the Russian Ambassador because Obama had just kicked out 39 Russian diplomats and Flynn was asking him to refrain from retaliating which the Russians agreed to do. The transition team met with Flynn before the call and talked about what should be discussed on the call. Sanctions was one of the topics. When Flynn saw the news report specifically stating that he had 5 contacts (which included dropped calls) he immediately knew that he was being surveilled. He then went to all of the transition team members and told them to say "NO" if they were asked if he discussed sanctions. He didn't lie to the transition team, he instructed them to lie which is perfectly legal regarding National Security information which is exactly what the call was. This was the hook that he dangled in front of the Deep State. This was the setup. It doesn't matter whether or not Flynn lied, he is authorized to do so to protect National Security info.
The ONLY THING that the FBI agents had ANY business questioning him about is about the source of the leak from his phone call. The FBI does not have the privilege to access National Security information, they are a criminal investigative agency.
So, you're right, it was a setup from the start. General Flynn took his massive green weenie and fucked the Deep State straight up the ass. The Deep State is trying to railroad him for lying when he was authorized to lie, so it really doesn't matter. But once they brought charges against an American citizen, they fucked themselves. It's fucking glorious. Flynn has probably been laughing to himself this whole time about how easy it was to fuck these people.