In fairness, it could also be merely a silly throwaway line. I know from professional experience that some organisations use language sloppily; they revert to cliche and platitude often without really knowing (or caring) how their words will be construed. And on its own, you could wave away the rude response and its implicit message.
But, you’ve made it clear that this may be a one-off payment, but it’s not a one-off instance of fault shirking. It’s not an exception, but part of a long pattern of behaviour, involving stuff ups, slights and evasions.
It’s easy, especially when you have no direct involvement with a work problem, to roll your eyes and accuse a colleague of being “over-sensitive”, hoping rather than knowing that their concern is trivial. It’s easy but often not wise.
Your organisation ignores this dodginess at their peril. My advice would be to keep on about it and maintain a record of everything that’s happened. If the problems get worse – which seems likely – you may one day be asked “Why didn’t we know about this?”
Make sure that you have evidence to back your response: “We did.”