The same thing happened to me when I tried to collect the verdelon 3. you'll have to go the very long way around, through Grande Pastura, Litore Torto, and a few other provinces, depending on what garage you're going to.
I just collected it with an Urga Postolka, while flying through the zone, and the nukes couldn't hit me. It was a long and painful flight back to my nearest liberated town with a dock garage at Colle Salrosa .
idk I guess it might have been the weight of the car slowing me down, and the game thought I was moving at top speed without the weight so the missiles tracked ahead of me.(The game probably used my throttle input).