Sorry for the double post, but I've been experimenting some more after work and I *can* reliably reproduce the issue from the attached save. I tried it at least 10 times. Here are the steps:
1. Load up the attached save.
2. Go to the 113 Aquarii System. In the upper right corner of this system, you'll find the fleet "Cruiser Squadron 1 (Achilles)" parked about 70 million kilometers from an Unexplored jump point. They are sitting on the "Wreck of Unicorn-E R59 class" which makes this really easy to demonstrate.
3. Pass 1 Hour. The NPR should reappear. Wait about two minutes and they jump out again.
4. Give the fleet a move order to Waypoint #3. They're in "United Combat Command" -> 1st Fleet -> Expeditionary Forces Command -> Cruiser Squadron 1.
5. In about 20 minutes the missiles will show up on thermals. They appear about 10 million kilometers from the fleet so you can watch them come in for awhile.
6. Pass some more time and you will see the missiles tracking unerringly towards the "Wreck of Unicorn-E R59" rather than the fleet which has now moved.
7. The instant the missiles reach the Wreck, one of my ships 2 million kilometers away explodes.
The NPRs really like this trick as they have repeated it multiple times now. They've killed more of my ships with this bug than they did in the entire assault on their home system.

EDIT: If anyone else runs into this, the trick is to accelerate TOWARDS the incoming missiles. They will go right past towards your original location (I think this is expected behavior, but a bit weird) and you have twice as much time to shoot AMMs at them. A bit cheesy perhaps, but there isn't much else you can do.