Bug: sometimes the fleet that picked up the probe and you pay them to retrieve what's yours, they may infinitely try to pursue you and do nothing on contact.
It renders the game nearly unplayable until you burn all the way and shake them.
Found the root cause of in-system in-faction trade disruption: random trade convoy of other faction lost
The most common ones are pirate and pathers. Since everyone hate them, even their tiniest trade fleet get crushed by other factions' trade fleet and it immediately posts -2 deficit to my own colony, which has no fault on my own logistic officers at all.
All trade convoy must carry something on both trips which makes this happen: my colonies are all self-sufficient except for organs, and in-faction supplied goods shouldn't get affected by outside traders.