As a general rule with Freespace, docking is weird. My assumption is that Scorpio 1 is in a wing - that's most likely to be your problem, as FRED doesn't check the other likely sources of problems, like docking paths and dockpoint incompatibilities at this stage.
But I'm assuming you want Scorpio 1 in a wing, so I would suggest making use of the jettison-cargo sexp instead. Assign it to the ship that Scorpio 1 is docked to, and select Scorpio 1as the specific piece of cargo (i.e. Docked ship) you want to jettison, otherwise it will dump everything else. Then you should be able to proceed as normal.