Yes, because the last thing he wanted was Flynn looking into what he and his henchmen in the intel agencies and the DOJ had been up to.
The FBI agents who interviewed him initially said they thought he hadn't "lied" to them. He was a bit circumspect, but the National Security Adviser is not typically required to tell mid-level bureaucrats what he talked to the Ambassador of Russia about. Mueller, taking his typical overly authoritarian view of the matter, decided to charge him with a "lie" that really wasn't. Flynn said he didn't talk about the sanctions, and he didn't. If you think he did, the transcripts are out - go find me which specific sanctions are listed in there. I'll save you the trouble - there are exactly none. Mueller did what he usually does - he saw a crime where one didn't exist by taking the broadest possible interpretation of what "talking about the sanctions" means. In Flynn's (correct) view, he was asked if they discussed the sanctions and they in fact did not get into any of that, but rather merely talked about Russia's potential reactions to them. Mueller (wrongly) interpreted that as having "discussed the sanctions" when, in fact, none of the actual sanctions were even mentioned. Any reasonable person would accept that as a reasonable person's reasonable interpretation of what he was being asked, but Mueller is not in the least, a reasonable man.
He didn't lie to the VP. He had discussed with the White House what to talk with Kislyak about before ever talking to him. That's what three star generals do. But the Russian collusion delusion was out of control by then and the White House was trying to tamp it down so they could get on with their work. So they decided that Flynn should fall on his sword, and take the rap for jumping the gun on discussing foreign policy with Kislyak in an effort t take the "Russian collusion" heat off of Trump; and so he did, because that, too, is what three star generals do.