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.
Was this just today? I run this on both sides every day and that's never happened to me on the villain side. I get the blue (royal) amazons on my villain and my heroes get the red (rebels).
It has been this way for me on the villain side (USPC) since AF2 launched. The only reason I'm noticing this now is that I finally have a hero alt that can access Patrol Catastrophe. None of the Amazons I rescue as a hero attack me.
For me on USPC it happens every time. I've never not been attacked for saving that Amazon. So ungrateful!
I've had it too, I just never thought twice about it since I've never had a hero that High of content.
I paid more attention to this on the past few runs. On the heroside, 100% of the time, you get allies on all 3 sides. On my villain, it was always an ally down the middle and to the right. The left one was always a rebel (red) amazon. Whatever was intended, the hero & villain sides should be equal.