Very annoying but working as intended. Only the owner of a mission arc is awarded the badge in regular game play.
For now it could help that all team members pick up the mission and autocomplete when prompted.
I checked the wiki and according to that after Marauders lines a Scryer tells you to Go!
Marauder: I'll find you, you little maggot!
Marauder: Even if I have to tear down this entire damn tower to do it!
Scryer: Go!
You just have to run to the door and exit to complete.
Malta Sappers in the Black Scorpion story arc are not counting for the defeat badge "Running on Empty'.
Their spawn name is: MaltaFake_Sapper.
Sappers that do count are: Malta_Sapper.