I had almost the exact same thing happen at my last shop, except the guy used a 6 inch torpedo level on my fixture plate. He swore the table was off by half a degree and wanted me to shim the whole setup, even after I showed him a .0005 indicator sweeping the plate dead flat. These inspectors come out of a class where they learn to eyeball stuff and then scare you with big scrap numbers. A bubble level has maybe a .5 degree resolution on a good day, which over a 6 inch jaw face is something like .050 of an inch, not a thou. The math never works out but they say it with such a straight face that you start second guessing yourself. You did the right thing by re-indicating right in front of him, because the part is the only argument that actually counts. Let him walk off without an apology, that shrug was probably the closest thing to one he's got.