This is present in 6.1 and frankly the only way to stop it is to not build jump gates then at least the madness is confined to one system.
The trouble is that if there is an opening on a world every colony ship sees it and then they all go there. There is no solution to the problem as it is a programming issue that needs to be sorted out, and the sorting out unfortunately is likely to become rather complex. Approaching the problem blind I see no simple solution. One that might work is that each shipping firm is polled in order (with a flag to keep it from all going to the first firm), and then if there is an opening its colony ships are polled in order with flags set to stop the polling once the number of onboard colonists equals the current infrastructure limit. The next opening would go to the next firm and so on.
With the current system you just get huge "dumps." Worse the infrastructure demand of the colonies is not sensibly addressed either. Basically it is an issue Steve has to fix in the game code, beyond not using jump gates you as the player can't do much about it.
I am playing 6.21 and do not have this problem. My civilian shipping is doing a good job of transporting colonists and infrastructure to my fledgling colonies. One difference is that I am leaving some of my smaller established colonies as destinations, so that the civilians have a variety of locations to choose from. This results in just a few trips to each colony. I start a new colony by sending 10 infrastructure to it on imperial (not civilian) freighters. The civilians then send colonists, and as the colony approaches the population limit they start sending infrastructure. The only way to get huge dumps is to build up a large number of civilian colony ships and then only have one open world at a time, leaving established colonies open spreads the shipping out. Forgoing any colonization for 5 to 10 years will thin out the number of civilian colony ships as they are retired. The civilians
for 30 years I was only colonizing solar system. It was more or less ok, since my civilian companies were only starting out. After I ran out of "perfect" worlds(Earth, Luna, Mars, Ganymede, Io, Europa, Callisto) I started to look for acceptable extrasolar planets. While I was surveying and building jumpgates my "7 colonies" were all set to "Stable".
No civilian passanger transportation were observed during this period. Luxury Liners were idling at spaceports. This is confirmed by absence of any tax income on Passanger Liners.
So my first question:
I thought that Luxury Liners would ferry rich citizens back and forth regardless of the immigration settings. Is it not true? Are they just mini-colonizers now? Or have I messed something up? Is it possible to get them working between established colonies?
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Once jumpgates were complete I contracted civilians to ship 100 Infrastructure from Mars to my first extrasolar colony, Cluntius Placidus-A II. I also set Mars to be "Source of Colonists" for a fairly short period.
Civ. freighters took the required ammount of Infrastructure and went for jumpgate. All civ. colonyships AND luxury liners took full load of colonists and were just sitting at Mars heading nowhere. My civilian lines are pretty rich. We are talking about 260 ships, of total tonnage: 10M tonns. A lot of them are colony ships, so...
After a while, once initial 100 Infrastructure was unloaded, ALL of civ. colonyships AND luxury liners decided to move people to their new home. And so they did: now I have 7.5M population on a planet with only 100 Infrastructure (supports 0.5M population). I can accept a "slight" overachievement, like shipping maybe 10% more colonists then required, but to miss 1500% is quite unnerving. What will happen after 30 more years, when civilian corporations will flourish from interstellar trade?
Hence my second question:
How to colonize right? Is there any way to ban some of the colony ships? Should I have contracted 10k Infrastructure in the initial shipment? How to create tiny colonies then?
The scenario described is exactly what I would expect to happen if you had a large number of civilian colony ships and only one destination. It is not a bug, just the way the world works. Once the 7.5 million colonists are landed, you should see the civilian freighters loading up on infrastructure. It might take several months to get straightened out, but it is due to the constraints you placed in the first place, not a bug in the program. I would suggest that you send a brigade or two of garrison troops to quell the riots.
A solution to your problem (prior to them landing) is to clear the civilian orders and reopen some of your smaller Sol colonies as destinations, this will spread the colonists around and slow the growth of Cluntius Placidus-A II. Civilians will not send colonists to a colony that is over the population limit. You can check the wealth screen to see how much infrastructure a colony is demanding. The higher the demand the higher priority it will get from the civilian freighters.
The only way I know to reliably ban a solar system is to change the empire possession (on the galatic map) to an empire that you are currently at war with. I have seen civilians violate a body ban, they are just sure you are lying to them to protect it for your self. But I have gone 20 years with a 0 cost habitable world in a system that I have told the civilians is possessed by the "Ancient Guardians" and never had a ship stray there even with jump gates on all of the jump points.