You tell them, and they refund you, and they look into their operations and figure out how they let bruised apples slip into a customer's order so the problem can be remedied.
Had you gone to the market you would not have bruised apples.
I value my time more than I value not experiencing the pathetically infinitesimal trauma of the occasional bruised apple (something I experienced not once in the 6 years I lived in Santa Clara and had 100% of my groceries delivered).
And yet somehow, FreshDirect's managed to stay in business since 2002.
When the options are taking the L to Whole Foods vs ordering Fresh Direct, both options suck. Fresh Direct just sucks slightly less.