I have a very interesting bug report. Unfortunately, I can't provide a save and it's not easily reproducible, but I think I have collected enough evidence to help track down the issue.
TLDR: Some NPR missiles with thermal sensors teleported about 2 million kilometers and detonated in a single 5 second increment. I believe this happened because my fleet was moving away at the time, the missiles reached my original position, reacquired me with their onboard sensors, and then detonated immediately, attacking my ships as though they were still in the original position. This was accompanied by a generic "Key not found in dictionary" error, but I'm not sure if it was the NPR missiles or my AMMs that triggered that.
Long Version:
The NPR missile in question is the "Kukri Anti-Ship Missile" a size 9 missile with WH12, speed of 55,000 km/s, max range of 104 mkm and, most importantly, a 0.25 MSP thermal sensor.
The situation is that I chased one of my local NPR's fleets to a stabilized jump point. They jumped out and my fleet parked 35 million kilometers off to wait for reinforcements. What follows is an abridged version of the Game Log when the NPR fleet briefly returned.
1894113097 "Missile Battle Fleet - Jump 002 cannot conduct a transit as there are one or more ships suffering from jump shock" Xcor: 719826778 Ycor: -449797692
1894113097 "Contact re-established with Hostile Ship contact: [AAÓ] XX Dmitriy Pozharskiy 001 19,999 tons 0 km/s" Xcor: 684865572 Ycor: -448150254
1894113256 "CS-07 Valour 007 has launched 13x Kukri Anti-Ship Missile from Size 9 Missile Launcher (30.0% Reduction) targeted on XX Dmitriy Pozharskiy 002. Range 35,000,000 km Estimated Chance to Hit 123%"
Here the NPR fleet jumped back through the stabilized jump point. You can see my original X-coordinate attached to the contact established message.
1894113276 "5x Kukri Anti-Ship Missile cannot locate its target. it will continue to the last known target location and use onboard sensors to search for a new target"
I didn't have a lot of AMM launchers, so I ordered my fleet to move almost directly away at its top speed of 9000 km/s. Quite a bit of time passes as missiles come in.
1894113821 "Updated Hostile Salvo contact: [AQ] Size 9 Missile x3 (Salvo ID3454) Thermal 25 55,000 km/s" Xcor: 688786222 Ycor: -448335003
1894113891 "CA-12 UNS Gawain has launched 4x SIM2-1C "Peregrine" 90kms from Size 2.0 Missile Launcher targeted on Salvo ID 3440. Range 1,736,791 km Estimated Chance to Hit 35%" Xcor: 683253554 Ycor: -448566936
At this point, you can see that the range to the missile is 1.7 million kilometers. You can also see that my fleet has moved a bit more than 1.5 million kilometers on the X-axis from where it was originally detected by the NPR ships.
1894113893 "CA-12 UNS Gawain attacked Salvo ID 3446 with Quad R30-50 Autocannon Turret Mk II. Range 10,000 km Chance to Hit 34% Shots 5 Missiles Destroyed 0" Xcor: 683236127.579917 -448571441.205602
Here you see just 2 seconds later the same ship attacks with a Gauss Canon at 10kkm. In that time my ship moved 17,427 km on the X-axis, roughly consistent with the speed of 9000 km/s. The missiles though appear to have moved over 1.7 million kilometers in these two seconds.
1894113893 "8x Kukri Anti-Ship Missile from CS-07 Valour 007 attacked XX Dmitriy Pozharskiy 002. Chance to Hit 100% Damage per Hit 12 Armour Hits 4 Penetrating Hits 4 New Target Speed 9,000 km/s" Xcor: -2101822936.46163 YCor: 806814233.320147
1894113894 "4x SIM2-1C "Peregrine" 90kms has no target and no onboard sensors and will therefore self-destruct" Xcor: 683417124 Ycor: -448491803
Here we see the missile detonation message, which has some pretty weird coordinates. I'm not sure if that is relevant, but from a quick skim of the log it looks like missile detonation messages usually have more accurate coordinates. You can also see that my AMMs self-destructed one second later, having never attacked, because the missiles jumped past them.
My hypothesis is that the missiles attacked my fleet when they reached my original position, instead of my new position.
I hope this information helps you figure out what happened because this seems like a pretty dangerous bug if NPRs are making more missiles with onboard sensors now.