If they are that bad, take a sharpening stone and lightly smooth out the rails. Don't take a lot of metal off, just what you would after sharpening a knife to remove the fine wire on the edge.
Do the cases show any signs of potential failure after firing?
I just went out of my way to try and scar the brass and it did scar the brass, but I pressed heavily on the brass against the rail and it marred the casing.
Being that the fire arm is not fired and I'm assuming you have close to a full magazine, the pressure from the spring in a new mag is going to be high enough to cause this scaring.
These pistols are built with tight tollerances.
The feed area we are talking about is going to be slightly sharp, but for it to actually damage the shell to an extent for failure, it would have to have some massive burs on it which would bite into the brass.
Now, when I first got my C9-A1, I ran about 100 rounds though it cycling the slide and left my magazines full for a day or 2 to break the mags in because they were so hard to low.
I cannot honestly remember if mine marred the brass any.
But as mentioned before.
We are taking a soft metal, brass, and pushing it against a hard metal and stoking the hard metal over the brass. It WILL cause scaring.
If you are worried about it and the groves are deeper than you feel confident with, then take a ceramic stone and hit the edges on the inside there and knock the burs down.
It is entirely possible they are sharp.
I'm not trying to call you a liar or anything.
But, the universe does weird things.
I can explain as to why these things are happening making excuses for the MFG, but, sometimes it's just something more simple than that.