Increase the cargo capacity of Tiny and Small planets?
It's just a bug of the minister AI caused in part by the way the AI clears orders when it has no room for a cargo transfer it had orders to do. Apparently the transport minister can get stuck on this.
If you're playing emperor and having trouble with your ministers doing this, you can order them to do something else with their cargo. Have you tried ordering them to drop their stuff somewhere that has room?
PvK