This makes a lot of sense to me - it's not even because the apology is logical, but because it's a gesture that shows the speaker is thinking of the other's welfare. There's a rule I have followed for many years when doing customer service - if the person is upset, apologize. It doesn't matter if you can't give them what they're asking for, or if they made a silly mistake. Just - make them feel better, then do what y…
To many, apologizing has become a automatic reaction and they now apologize for everything. They don't say the person is thinking of others, nonsensical apologies mean that the speaker isn't thinking anything about you and just wants to get on with their day.
You did it in the next paragraph. You're not sorry, you probably don't give a damn about them, you just need to move on to the next person.