It's my opinion, but I'm going with USADA played a larger role than people realize.
Program started Mid 2015, a couple months later she fought Bethe Correreia in Brazil(..Bethe in Brazil, not a great metric and only a month or two into the program)
Then fought Holly that November. Much more nervous/mentally weaker, and looking much weaker in the Octagon.
You can argue Holm and Nunes were just that massive upgrades from competition, and I won't argue that, but if I had to bet money, I'd put it on her being another USADA victim and it affected her performance and mentality.