I tend to say "We're sorry for the trouble this is causing" combined with "We're working to get this resolved." - since it feels less stuffy/less like a canned response line.
Nothing grates on me more than that phrase. I hate it so much. It's so canned, insincere, and dismissive. I like Manuel's better, with Fernando's edit. Look up apology structures -- say what's really happening, then say what you're really doing
