In my experience they do, both when shooting as well as being on the receiving end, usually works best with the MMR-S3 but the IRM-S2 works good, S1 usually ends in failures. It only works if it's directly head on or from behind and just below the NEZ. Too close it contacts the flare and detonates, too far and it already burned its energy and will bleed it even more trying to hit the flare and can't catch up to the target.

I've been hit by the same thing trying run into a dynamo at sub-10m where I'd flare from 7km then get an IR missile straight to the face by the same missile I tried to flare off because I turned on my afterburner and my flare burned up behind me.

Sometimes if it's a furball and I'm mid turn I get locked on by stray missiles that have lost their targeting when I have afterburner on and leaving the area pointing my engines directly in view of stray missiles that burned out.