I made a scene and copied the activities.ini from the base, edited to have my custom clones in it. Now, the problem lies in that it won`t work. The normal robot 2, the green clones and skellies are dropped of instead of the custom clones. Changing Skirmish Defense in the base activities to something else, and setting the instance name in my activities to Skirmish Defense solves the problem, but makes them show up in every other map too.

Am I now supposed to blame data and wait for the next build for this problem to be fixed, or is there a solution?

Activites.ini doesn't allow customization per scene; wait for the next build.