What the Times story does not say is what Flynn said. But the logic of the report certainly leaves the impression that Flynn was less than truthful. If that's the case, the Flynn's dismissal just went from being a political scandal to major legal jeopardy. You can't lie to the FBI and people are routinely (often too routinely) prosecuted for doing so.
In the Times words ...
F.B.I. agents interviewed Michael T. Flynn when he was national security adviser in the first days of the Trump administration about his conversations with the Russian ambassador, current and former officials said on Tuesday.
At the risk of stating the obvious, this interview must have been in the context of the much discussed but still little understood counter-intelligence probe scrutinizing Flynn's communications with Russian government officials.