Yes, some times you encounter teams for which you don't have a counter. It happens until you have built a variety of teams for different situations. Depending on the strength of the two teams empire teams can sometimes beat geonosians.
I don't know which modding guide you followed, but maybe it's time to get a better understanding of mods. It will help you in GW. Don't underestimate their importance.
Also, it will be worth the investment to gear up some scoundrels to improve your credits income from credit heists. Boba Fett is still an MVP there and bountyhunters and ST Han are required to unlock some legendaries later. The earlier you're able to beat the top tier of credit heists (there may be some level requirement as well) the more return you gain from your investment.
