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1) Refine more than 4 SCU of material and set the Clipper as the delivery destination.
2) Wait for the refinery to complete the job; 4 SCU crates (sometimes 8 SCU crates) will appear in the Clipper’s cargo bay.
3) Try to sell the cargo; the kiosk requires a manual offload (No option for auto-offload).
4) The crate cannot be taken out through the ramp.

What happened
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Refining over 4 SCU to a Clipper produces 4-SCU or 8-SCU crates that can’t be manually offloaded.

Attempts were made several times at Levski to force the auto-offload option to appear—both with the ship stored and with it parked in a hangar—but it never became available.

This completely breaks the ability to transport your own refined goods.

What should have happened
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The cargo grid should be filled exclusively with 1-SCU and 2-SCU crates, since the entry ramp was intentionally designed to prevent 4-SCU and 8-SCU crates from fitting.
This would be the easy fix and consistent with the intended design choice; the logical solution would require a partial redesign.

Workaround
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The only workaround, unfortunately, seems to be avoiding the Clipper for transporting your refined goods.