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1) have a ship with cargo space
2) place a vehicle on the cargo grid
3) take this ship to a location that allows you to autoload cargo containers
4) fill the cargo hold of your ship with wares using auto loading (selecting the ship directly in the commodity kiosk)
5) retrieve your ship and look into your cargo bay

What happened
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The commodity kiosk that initiated auto load did not care that the cargo grid was blocked by a vehicle and just placed the containers on the cargo grid anyway. This cause the vehicle in the cargo bay to collide with the containers.

What should have happened
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the commodity kiosk should not have been able to load the containers into a cargo grid that is already blocked by something else

Workaround
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do not use autoload or be sure not to have anything on your cargo grid while using the feature