I accidentally found an exploit today ;D Given that it is technically not a bug, I will not follow the guideline :P
[Story-Spoilers!] I played the Order main quest until tasked with conquering an alien system adjacent to their capital. Realizing that I would need a few more levels and bucks, I went to freedom territory and finished a few old quests. I still had the quest to join freedom (Got that one after joining Order), so I went to their capital and talked to the recruiter, not being sure if I could maybe doubledip on factions. I changed factions, but can still buy mercs from the chief of Order and get money from every Hive destroyed. I also got twice the quest reward for getting the device that enables travel to the aliens territory.
This is actually a bug that was introduced in v1.2.1
It is already fixed and will be in the in the next version.