This is an odd one. If you end up with wormholes that share destinations (like the pair in this screenshot) sometimes you literally can't use some of the phase lanes.

In the above example I tried to use the lane from "Telesio" to the star, and my ships insisted on taking a route through the other wormhole. I tried putting them in different places inside the gravity well, but that didn't seem to make any difference. Likewise for the gas giant in the upper left. Oddly enough I didn't have the same problem from the other end of the wormhole (Kahnia).

I'm listing this bug as 0.76 because I haven't replicated it in 0.79 yet, and I don't know anything about making custom maps. But I'm guessing it's still present in 0.79.