Not if they're doing the labor, it's not costing you anything extra, and when they are done it looks as good as new.
Stone veneer is pretty...um... static, so assuming they install it properly, and make it look good (which takes more work the second time around), you should be fine, just don't sign off until you've had a third party inspect the (second) install (unless you know what to look for as far as shoddy workmanship) to verify that it was done right... afterall, if they were careless enough to install it in the wrong place, how do you know what other places they cut corners...
I guess they are also going to repair the damage to the areas they installed (so you aren't missing an exterior)
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