In the villain version of the final encounter in the Gotham Hospital bottle, the Amazons you free from the cubes that spawn from the East side of the map are loyal to Wonder Woman's faction, not Hippolyta's/Circe's. So when you free them, as thanks, they start attacking you. (Reminds me of the cutscene from the East End Regal Hotel instance where the bat rescues the scorpion and gets stung as thanks.) In the hero version, all three Amazons you free are from Wonder Woman's faction, so they all join your fight. It's not a deal-breaker as it's easily overcome. However, between this and the placement of the initial field report where it's surrounded by WW's Amazons, it's yet another hurdle that villains must face that heroes do not.