Pay really close attention to this exchange:
Flynn: We have to eliminate this common threat.[ISIS, AQ]
Kislyak: Now FSB and GRU are sanctioned..does it mean that US isnt willing to work on terrorist threats?..Because that's the people who are exactly, uh, fighting the terrorists?

2/ there are two separate issues.
A) Did Flynn and Kislyak "discuss" sanctions against FSB and GRU?
B) perhaps more importantly, everyone to date (including both me and NYT) viewed sanctions against FSB and GRU as "symbolic" http://archive.is/n1kjG , whereas Kislyak interpreted

3/ sanctions against GRU (military intelligence) and FSB, as a decapitation by Obama admin of Flynn's long-term objective of Russian-US cooperation against ISIS and AlQaeda in Syria-Iraq, where both ISIS and AQ then controlled large territories (Aug 2016 below from Wikipedia)

4/ as Kislyak pointed out, it is precisely the two agencies sanctioned by Obama (GRU, FSB), and, perhaps, especially military intelligence GRU, that are "the people who are exactly, uh, fighting the terrorists". So any attempt by Flynn to coordinate with GRU v ISIS was prohibited

5/ I also noticed a curious detail about sanctioned intel officials listed by name in Exec Order. All four were noted in Dec 29, 2016 NYT article as being GRU (military intelligence) officials, no FSB officials.

6/ remember that Flynn's own intelligence background was in military intelligence DIA (Defense Intelligence Agency) where his direct contacts would be GRU. So the Obama admin sanctions didn't merely sabotage intelligence cooperation in general, but Flynn's contacts in particular

7/ in this context, it's worth recalling that Brennan, Clapper et al had attributed DNC hack and delivery of emails not merely to "Russia", but to GRU specifically (to whom they attributed "Fancy Bear"). As of Dec 29, the Obama admin hadn't provided Flynn or transition team with

8/ any intel supporting the attribution of hack/WL delivery to GRU, nor do such actions, when one thinks about it objectively, seem like logical activities for a military intelligence service. Maybe for Russian equivalent to Brennan, but not Russian equivalent to Flynn.

9/ accompanying Obama Dec 29 announcement of sanctions, expulsions was tech analysis (discussed here recently) purporting to show "tools and infrastructure" used by Russian "civilian and MILITARY intelligence services", info that they presumably expected to end attribution debate

10/ it didn't. Their technical information was a fiasco. NOTHING in it connected to military intelligence GRU or even Fancy Bear, their supposed vehicle. Vast majority of listed malware hashes was Ukrainian open source malware, available for purchase on internet.

11/ the embarrassing identification of supposed RIS military malware with Ukrainian malware available on internet was reported almost immediately (Dec 30) by Wordfence. While this didn't attract any attention in US mainstream media, it must have caused cold chills for Obama intel

12/ at some point, Flynn, as incoming NSA, would demand that attribution of DNC hack and Wikileaks publication be examined by specialists that he trusted, to verify whether the seemingly implausible attribution to GRU was warranted. I doubt that Obama intel leaders wanted that.

13/ among other results of the decapitation of Flynn by intel officials and complicit media, there has never been a first principles technical re-examination of Brennan's attribution of DNC hack/Wikileaks publication to GRU by specialists that Flynn would have trusted.