I don't think they are, but it's the right thing to do. One would hope the banks would be understanding enough about the situation (haha, I know, right?) to reverse the fees. But even in that case Twilio is still causing you to, at a minimum, call your bank, wait on hold, spend 15 minutes getting transferred around to someone who has the ability to reverse the fees, etc. If they want minimal impact for their customers, they'll just reimburse the fees.

I played this game with Dreamhost and SunTrust back with their whole billing debacle in Jan 2008. Dreamhost didn't respond to my support requests to reimburse "non-sufficient funds fees", The bank manager at SunTrust said that regardless of the reason funds weren't available in my account when the other transactions posted, so the NSF fees that I was incurring were legitimate.

In the end I think I paid a little over $300 for their mistake.