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1) Lower The Cargo Elevators
2) Try to put 1 or 2 SCU boxes on the Cargo Elevators

What happened
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1 and 2 SCU Boxes bump against the bottom of the Intrepid because the ground clearance isn't high enough so you end up damaging your ship in the process of loading and unloading boxes.

What should have happened
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A better ground clearance so the ship doesn't get damaged by simply loading cargo.

Workaround
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There is no workaround, the chance of damaging your ship is high.