Flynn didn't make much friends during his short term. He repeatedly lied on two issues (his talks with the Russian ambassador and the security clearance for his son) to Pence and others and it has been claimed that his management style was chaotic. The lie about his son was very likely the most harmful as it was such a a black and white issue and so sure to be found out.
But what has been very little discussed until now is the role of the security services. We do not know what exactly happened but I am afraid it happened the following way:
The security services had his conversations with the Russian ambassador on tape. They invited Flynn for a discussion about something general like his "Russian contacts". They did not tell him they had his conversations on tape. They did tell him that they knew about his contacts with the ambassador and they told him that that would have violated some very old law that forbids citizens to do diplomacy. They did not tell him nobody has ever been convicted on basis of that law and that prosecution on basis of it likely wouldn't hold. They didn't provide him time to rethink his conversation with the ambassador in the light of this information - that must have been new to Flynn. Neither did they tell him that lying to the FBI can be heavily punished. So they had an "interrogation" where they only asked what they already knew and where they deliberately brought Flynn in a position where many people would lie.
In my opinion this should have consequences - for all the intelligence officers involved. Intelligence officers are there to serve the government - not to set boobytraps for it.