There are 2 AP bugs at work here.
The ship comes out a gate, plots a course for the hub, and ignores any obstacle in between that that a blind man with a long stick would tell you to fly around not through.
Having detected the obstacle, the ship avoids too late, to radically and slides into the obstacle, then cannot get away from it and then head buts the obstacle until one on them dies, usually the ship.
I've actually defined it as 3 bugs in the list I'm doing atthe moment.
The idea behind the shields of the Gunbus was to ensure it lived through one of these, but alas, only 10gj shields seem to guarentee survival.
As said, placement of the hub so that nothing obstructs it, makes this less likely to occur.
My complexes are all built on a single plane, with the hub sticking way out like a netball pole, far above or below the plane of the stations. Because there is nothing around to obstruct it, the only ships that have a problem are those that undershoot and hit the connecter going to the stations.