Jim's explanation is "right on the money". At my working place we have had that instance happen to us on numerous occasions.
It's always good practice to adopt a helpful attitude towards the customer. Someone should talk to your customer and convince them to eliminate the "reference" altogether at that particular dimension location and to go by the tolerance chart on the manufacturing print, if there is one. If not, one should be added in parenthesis at that dimension location (i.e., (+.005/-.000) ).
The most common ones I've seen on the tolerance charts go like this:
.xx = +/-.030, .xxx = +/-.005
Another option, which I myself prefer to see, is GD&T tolerancing.
If that doesn't work, getting a sub-component from the customer to fit test your manufactured part is another option.
Yes, some customers, you just can't seem to win and they will "knit pick" you to death. Hang in there! I feel for you.