Is the "Discard" in the mission breakdown an action or is it possible it was meant to be an action? Feels like it couldve been worded differently if all you had to do was enter the space and get the points.

Because the rule does not incur an action cost, it does not cost an action.

Just interpret it literally - When a figure carrying a crate enters the extraction point, do what the rule says.

It could've been written a little differently and have the discard be a cost, but because each figure can only carry one crate, this works just fine.