I found the following on a page about sapphires:
Pure corundum is colorless, but most corundum contains minute amounts of chemical impurities called trace elements. Blue sapphires are colored by a combination of the trace elements iron and titanium. Iron and chromium together result in gold or orange sapphires, and when chromium is the only trace element, it makes a sapphire pink or a ruby red.
So it depends upon what trace elements are present as to what color a piece of sapphire is. So it is possible that when the character in question shaped the rose he removed pieces of sapphire that had other trace elements in them (to make the rose a uniform blue color) and that those fragments had other trace elements mixed in.
So one had little or no trace elements and was clear while another fragment had a trace of chromium mixed in with the base material of the sapphire and was therefore red in color.