C: We don't have it in anything but a 9 right now.
C was trying to say that they don't have it in (the store). But, "the store" was left out. am I right?-- Sort of; 'the store' is not the only phrase that could have been omitted. The phrase 'in stock' is also possible.
"We don't have anything but a 9in right now" -- Here, "in" could mean "in stock" or "in the store."
But that's not how the original example was structured.
The original quote was "We don't have it in anything but a 9 right now." -- Here, it means "We don't have it (this item) in any size except a 9." The "in" refers to "in a size x," no
Right -- if you assume "We don't have it in." is in fact a complete sentence, then your interpretation is correct. But then what do you make of "anything but a 9 right now"? I guess I was more willing to assume a misplaced period that a whole meaningless clause.
If everyone actually punctuated and capitalized correctly, it would sure take some of the challenge out of this!