The Logan Act makes it criminal for any unauthorized citizen to negotiate with any foreign power against the interests of the USA.
When Flynn did so, Trump had been elected but not sworn in. That’s the kicker.
Then, Flynn lied to the FBI about those contacts, another crime.
Additionally, Flynn was not registered as a foreign agent, and that’s against the law also, to negotiate on behalf of a foreign power.
The FBI did wiretap a few calls between Flynn and the Russians but there was only very minimal incrimination.
But, Kislyak and other Russians were reporting back to Russia, contacts of a much more substantial nature that were clear violations of the Logan Act, that happened before Trump was sworn in.
So, the FBI figured out that Flynn was meeting with the Russians in person to avoid FBI eavesdropping, that’s what Flynn lied about. Instead of about 4 conversations with the Russians, there were about 30, mostly face to face, no records.
In fact, the Russians agreed to change their tactics at the UN because of an agreement with Flynn and his Trump contacts, before Trump was sworn in, that’s against the law, the Logan Act.
Additionally, Flynn was not registered as a foreign agent, and that’s against the law also, to negotiate on behalf of a foreign power.
Whomever, on the Trump transition team was Flynn’s handler is in big, big trouble. If Trump was told about any of these goings on before he was sworn in, he was obligated to tell the Justice Dept./FBI.
If not, that’s conspiracy and/or obstruction of justice. It may seem petty, because if they had waited just a couple of weeks, all these contacts would have been completely legal.
As a non-expert trying to figure out if there is anything to all this—my own meager understanding is that the Logan Act is kind of a dead relic except for talk about it. I read that there were only two indictments ever issued for it, and zero convictions, with the last attempt being in 1852. And I have also read that in 1062 a Federal court mentioned in passing they thought it would not survive a constitutional challenge.