Drives me nuts when AS uses that verbiage when I'm actually in the right.
AS is the only airline that I've experienced this with (and I've experienced it more than once with them). It certainly is very off-putting and has left a negative impression of the airline's customer service in my mouth.
That's why I've said in the past here that AS is all smiles up front but then poor at fixing real issues, whereas other airlines--UA and AA being the main ones I've dealt with--come off a little gruffer at first but are usually easier to deal with on the back end (when what I'm asking for is actually within policy or when a policy exception makes rational sense) without any of this "Well, we are very reluctantly giving you this one-time exception that we really don't want to do, and by the way, your account will be noted that you're not to be given a little grace like this in the future next time you call us whining for something" feeling that I get when I call AS. And it's especially bad when they make you feel that way and you actually are in the right, as the OP was.
That's an element of the corporate culture at AS's call centers that I really don't care for and wish they'd improve.