Issue: ships coming from hyperspace (capital ships expecially) go to 99.9 km
On this I have a very bad fight with my young apprentice, importing TIE Fighter mission and plotting some custom on Allied for a while until I noticed a simple truth. Distance count! When you set entrance for you ship, you should check the spacing slot in formation. If a ship is bigger of the space you issue in there XWA will manifest the bug. Same is if the "formation space" will go through existing object in space.
For brief, for ships, expecially big ones, flying solo, put that number to "0" and you will never have the issue.