Check if there is a fleet jumping back and forth between the same two systems. NPRs frequently get themselves "trapped" in this way when an order to, say, refuel at the nearest colony causes them to jump into a hostile fleet (alternatively it may have something to do with the system danger rating, I'm really not sure), and since NPRs can instantly re-jump they flee through the jump point, and then repeat the process over and over while trying to fulfill their orders.
Usually the problem can be solved by relocating the fleet involved so that they cannot immediately jump again.