I'm certain that only the Neinzul Rocketry Corps are the only faction that can employ warheads against a Human.
So what's likely happened is that you accidently put a planet on alert that housed a Rocketry Corps Silo, so this silo is now firing EMP and L Warheads at you on a regular interval.
The only way to counter this is to place some expendable turrets near the wormhole entrance to blow up any rockets as they come in, or place some stealth units in the offending system to shoot the rocket as its fired.
Hence why I disable NRCs.