You're comparing apples to oranges here @truth_seeker Obama was already President at that point of time so the Logan Act did not apply.
No argument over that. (although at the point Obama's reelection was not assured, since the time of the contact was Mar. 2012-election year)
OTOH it is being suggested that the CIA recorded the call in question, and released it to the media to discredit Flynn.
Flynn represented an agenda of peaceful coexistence through cooperation with Russia, and the CIA represents an agenda of permanent low level conflict, to benefit the Military Industrial Complex that Eisenhower warned of, and that NeoCons also represent.
I am NOT claiming I know all the factors, just passing along one version. Dennis Kucinich among others, suggested this and he is no friend of Republicans.