US intelligence is monitoring Russia's ambassador--of course they are, not least because he's known to be involved with Russian intelligence--and catch him talking to an American about undermining US foreign policy. So they have to... willfully ignore it?
But US officials knew Russia conducted a big intel op against the US, and knew this convo with Kislyak was hidden from the US gov. Not finding out who it was would be a dereliction of duty.
That's why clutching pearls over them finding out who it was is silly.
Reasonable to find out the name of an American in a US intel intercept if there's probable cause for concern. Flynn's convo with Russia's amb after Russia conducted an anti-US intel op definitely qualifies.