The 'Playing God' singer admitted negative comments by brothers Josh and Zac Farro - who left the band last month - surprised her because she thought their departure was amicable.
Responding to the brothers' claims they were "always treated as less important", Hayley said: "I don't know if I got a phone call or an e-mail, but I woke up to it, basically, and that sucked, and I was not happy. And yeah, it hurts, because what we were told was that they weren't happy, they didn't want to do this, and you can't be mad at someone for not feeling something.
"But then when it really became about all these other things, I was very surprised and kind of felt led on, almost. We've been doing this for six, seven years now. I don't think any of this has been in vain, for any of us ... and I don't think anyone should discredit it."
Guitarist Taylor York also admitted he was uncomfortable with Josh and Zac's claims.
He added to MTV News: "It was really hard to read, just because it seemed like a lot of the stuff was pretty irrelevant to what happened. I think that was the weird thing, 'cause it just didn't seem really necessary."
However Hayley - who dated Josh from 2005 to 2007 - said she, Taylor and bassist Jeremy Davis are determined to put the controversy behind them and will now focus on making the band better than ever.
She said: "You feel every single type of emotion possible when something like this happens with someone that either was - or is - very close to you, you just feel everything, all at once. I've never felt so... I don't know, I couldn't even figure out how I felt.
"But you've just got to know that what's important is the three of us are still here, and that we want to do this, and that's the positive part about this."