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- Broken Base: As is usually the case for Steam Early Access games like Prison Architect and Planetary Annihilation, the game hub is sometimes prone to complaints about the Alpha's price tag. The same reasons for refuting the argument crop up as well, with the added benefit of Spacebase DF-9 being slightly cheaper than the previous two games.
- The reveal that Alpha 6 is the last update (bar bug fixing) has lead to many upset fans who were expecting more features implemented. The release of the source-code with version 1.0, and the message that "any new content for the game will now be in your hands", hasn't exactly won over many people.
- However a group by the name of "Derelict Games" has released Unofficial Patches/Adding features that were promised by doublefine. Though as of 2016, the group appears inactive, and the project abandoned. The group released one final update in 2018 before officially disbanding.
- Complacent Gaming Syndrome: By now, some users would have a favorite part of the galaxy to deploy, and stick with it. Additionally, there is one location in the lower middle of the western spiral that contains extremely high amounts of stellar density, low threats and magnetic inteference, and is extremely close to the warp gate. Most players who've found that area would stick to that zone.
- Scrappy Mechanic: As of Alpha 2a, the mechanic of other bases showing up out of nowhere and attaching themselves to the player's station has proven to be rather unpopular with players.
