I have a JTV-69, which uses an aggressive wrap (I assume that's what the previous poster means by "choke") over the bridge saddles and have never seen a string break at that point. After 8 months of hard playing there are no visible grooves on any of the saddles. It almost sounds like the castings on your bridge were not correctly hardened during manufacturing.
Filing does not seem like a particularly good plan. If the unit is under warranty, let Line 6 deal with it. Otherwise, I'd investigate replacing them outright.
I was referring to a point where the strings sit at an angle on the bridge, like a point where it's being choked at a sharp point to where it basically cuts the strings over time.
I had to lessen the action on my 600 to reduce the choke as it seems like it was cutting the strings by sitting on a sharp point in the saddle/piezo.
You don't want any sharp edges choking your string and leading it to be cut over time from constantly vibrating on that choke point.