It is exactly to prevent such a thing that I specialized all my colonies. Some colonies were built with the sole intention to mine it so it would produce so many ore my ships could not lift them all at once. After a while I just sent more ships to compensate, on a single trip, to grab the extra ore.
When you have several colonies sending ore to the Calypso like that you don't really need to bother with ore management anymore. Mass drivers are in theory very interesting but their output is very low and it take a slot both on the Calypso and on every colony afterward. I ended up not building any, in the end.
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