"X" indicates an item that was sent to a discounter or liquidator such as TJ Maxx, Marshalls, the now defunct Filene's Basement, etc.
Although I've never seen manufacturer defects, items with "X" aren't eligible for any warranty service and I also don't believe Coach will service them for a fee either.
My guess is that they were sent to discounters rather than their own outlet stores because quantities may have been to low for the outlets and some may have been shopworn or used.
But as long as the "X" stamp is on a genuine bag, authenticity isn't an issue. (I've seen 1 or 2 fakes with X but it's possible they were switcheroo returns that Coach stamped and liquidated.)