Flynn was also hit with a violation for not registering as a foreign agent when he consulted with Turkey (this was an Obama admin "error" that allowed them insurance over "rogue" generals like Flynn). He would have been forced to resign for in an embarrassing and highly visible scandal that would have left him comped, even though this was later cleared up. No one, other than Trump himself, seemed to harbor more hatred from the left and C_A than Flynn.
IMO Flynn knew nearly everything, he knew they would force him out on the Turkey issue anyway or simply make up a scandal (#MeToo anyone?), so he publicly lied to Pence (who probably wasn't in on it) to have Trump fire him and set traps for Yates, McCabe, Strzonk and other bad actors on his way out.