It is indeed not gamebreaking and just a small annoyance.
In mission 3 at the last opening before you take out the pirate base, half my fleet got stuck by only a short move order from one side to the other, no steps involved. This happened both when ordering ships in groups and individual ones. Some of them find their senses again when you move them back, but especially the XL class ships tend to stick to the looping for a while before returning to normal. The neutral XL's just outside this entrance seemed to be the worst culprits after being captured, as they're hovering above the station points and have to move down quite a bit before entering.