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1) Acquire a ship with cargo space (in my case: a C2)
2) put a cargo container inside the ship. Make it much smaller than the maximal total of carried cargo.
3) Place the container into the ship, but keep it away from the cargo grid. (in my case : 8SCU between elevator and ladder)
4) move to lokal Administration or TDD
5) fill your ships cargo grid with as many of the tallest containers as possible (in my case : 20x 32 SCU) using Autoloading
6) after Autoloading has completed, retrieve your ship
7) empty your ships cargo hold manually

What happened
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Autoloading is likely to create a total mess in your ship. For me, it has caused many containers stacked inside each other. Some slots will remain empty (though containers are stacked on top of empty slots) and some lots will hold more than one container in one position. If containers happen to stack like this, they may behave differently if you attempt to extract them. Sometimes, they shift away to the side and find a different space to occupy, and sometimes they lock each other in place.

What should have happened
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every container should be positioned by itself and extractable without collision issues or tractor beam malfunctioning (as is the case with stacked containers)

Workaround
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Attempt to unload other containers first. Attempt to approach locked containers from different angles. Try to free up the surroundings of locked containers to increase the chance of them shifting into empty locations. If all fails, claim ship to get rid of tight locked containers.