You must have read a different transcript. This one clearly shows he discussed the Russian sanctions, which he then lied to the FBI about. It doesn't have, like,
"the snows are deep in Stalingrad, comrade", in it, but it shows he did the thing he pled guilty to, and apparently didn't tell Pence about.
It would not have been a crime if he didn't lie to the FBI about it for sure, although it would have looked like he wanted to roll back Russian sanctions during investigation into them interfering in the election. I presume he didn't like that look, so lied.
Edit: I've now read the whole thing. I think this was released to burn Flynn. I don't understand why they released it otherwise.
Flynn told the FBI he didn't even know about the sanctions at the time of the call, but here he is, discussing them in a backchannel. I have to really be honest, @
TCinVA, I'm not trying to pick a fight but I don't think you read them if you think this clears him. It burns him. Whoever released this in the Trump admin wants to make sure people know he did it. My $10 is that it was Pence.