Audrina gets a lot of flack for her stupidity when she doesn't catch on sooner that there was no first Audrina, but honestly, she's a nine-year-old girl being gaslighted by her entire family, zonked out on medications she doesn't realize she's taking, suffering through faulty electroconvulsive therapy, and dealing with the trauma of being raped. She's undergone a terrible experience that she would just as soon forget, and she's trapped an environment where people actively support and foster her forgetting. When confronted with even the most obvious evidence of what happened, she goes into defensive mode and tries to explain it away by any means necessary—and as a child, some of her explanations do not subscribe to adult logic. Even in the climax, when Papa finally tells what happened to the First Audrina, adult Audrina is totally clueless and comes to two or three ridiculously wrong conclusions before finally being told outright she is the First Audrina. She's not stupid—she's a traumatized child in deep denial. As for why she doesn't catch on as an adult, it's possible that several decades of these kinds of mental gymnastics have turned denial into a habit. (As for why Audrina didn't get various other hints that Vera was really her half-sister or that Arden was kind of a douche or that Billie was hiding the fact that she has no legs, though...well, maybe in some respects she's just not that bright.)
That can also be attributed to the brainwashing she's been through. Everyone lies to her so often that she has no idea if or when someone's being truthful.
Vera's oversexed behavior, especially at such a young age, is often very indicative of having been sexually abused. Audrina might not be the only rape victim at Whitefern. Even worse, it might very well explain how she knew which boys to set upon Audrina—perhaps they'd already raped her and she offered Audrina to them so that they'd leave her alone.
Recall that Vera has installed a lock on the inside of her closet...
