I can provide another savegame as this is driving me mad in my current one.
Ark one, space planes, Raptors, V-wings, other fast, preferably long-range units for kiting purposes. Ark one's knockback makes this a really potent combination. Overdrive factory thrown in the mix for added effect.
I'll take the group into a planet, drop back a bit, issue move orders, and start kiting. Enemy fleet follows me around. As long as there is another, successive move order, there's no issue. However, once the fleet reaches the end of its travel path and there's no more move orders queued up, a decent chunk of the ships usually fly right back to the previous waypoint I set for them, which is inevitably right into the enemy's wall of ships.
I've personally only noticed it with very fast units. ~1800+