Cyberduck by default opens one connection for its Browser and then another connection for each transfer.
Thus servers which limit the number of connections will report problems.
I just looked into the Preferences - under Transfers/General there is a "Transfer Files:" option. Try selecting "Use Browser connection" instead of the default "new connection".
A specific number of allowed connections should be an added feature, with
the ability to reserve one connection for the browser.
I use several servers that allow a maximum of 2-3 connections. If i use the default setting for transfers, all my allowed connections get immediately used, and other files in the queue all try to hammer in as well, which tosses up
errors on my end, as well as irritating the administrators on the other end with me hammering their server with connection requests. I can't queue anything else up anyway, because my browser connection gets used up as well.
But setting to "use browser connection" isnt optimal either, as then I dont get to use the Transfers window.
A "Maximum Connections" field would fix part of it. A "reserve browser connection" checkbox would fix the other. Along with the underlying required functionality as well of course.
These features being missing mean that i have to fall back on Filezilla for anything i need to leave running over night, because there i can manage my queue. Cyberduck is far superior in every other way.