Oddly enough, I had the exact same issue, every single time I sent my 2 stilettos against an enemy that would engage my fighters (with the geoscape message: xxx is attacking yyy) using 2 stilettos with default missile loadout and 2.4 version....
Since I disabled the message setting (on geoscape) so that there is no "pause" when I'm being attacked, it's smooth...
Could totally not be related, but I just don't have the problem anymore after 8+ hours in that game.
Just my 2 cents.