This isn't Entrenchment specific.  I've always noticed that when I set a factory waypoint to a ship (such as a fleet leader capital), the new ships never react very fast to the fact that the waypoint is moving around between gravity wells, and they sometimes overshoot the cap ship and jump one or two grav wells too far before realizing that they missed the waypoint.  Then they'll turn around and come back to try to catch up to the fleet.  I can beat this with micro, or manually setting waypoints to different planets as I go along, but I can imagine this type of behavior should be easy to improve with some minor code changes.