As I understood it, shipping disruptions could come from even exports and imports: IE - a merchant fleet going outbound to another faction planet gets destroyed or a Hegemony merchant fleet heading in-bound to your own planet gets destroyed. Perhaps that's what is happening to the OP where an export fleet got blown up.
The needs are met by local production (Kalico transporting the goods to Rin), but I wouldn't mind if it functioned as you suggested; just as long as the first stop they make on their outbound journey is the closest one (whether your own colony or another one). Might even be interesting if there were escort options that can be set per industry where you can divert some of your system security patrols to escorting important (profitable!) goods to their targets safely, or make sure critical imports also arrive.
I would of been ok if perhaps the cause was a large pirate force happened to drop in on Kalico (it is a strong enough gravity well I believe), and destroyed the merchant fleet before it could reach it's target (though it is a VERY small distance), and to be fair my patrols aren't particularly strong yet even with the concentrated fire power of 3 stations in such a small area, but having a malus on my colony just because kind of seems a bit rubbish.
To be fair though I'm struggling to get money and was only just scraping by at around 15k credits a month, but this disruption dropped it to -27k credits when I have less then a 1/4 million in credits, so it really does hurt my finances...and there doesn't seem to be a good way of handling it? (I'm still open to other ideas!).