A bit of an update:
First, here are some pictures of the punctured MRE's. If you look closely, you'll notice that not only is the outer clear bag punctured, but so is the pouch of food underneath. Granted, it only appears to be the 'snack bread' pouch and not the entree, but still, the manufacturer's box stapling technique should not ruin 1/4 of the MRE's in each case.
And here are some of the offending staples that caused the punctures:
Now for the update. A very Indian-sounding woman from Munire called me just as I was leaving work today. She was a bit difficult to communicate with but she did offer that if I sent photos of the punctured MRE's they would send me replacements. She said they would try to replace with the same entree meals, but that was no guarantee. I hope that they don't stick me with the crappy ones. While a bit of me hopes they would offer to send me a full replacement case of MRE's, I'd be satisfied if they just made it right by sending me 3 replacement MRE's. I just emailed them the photos, so we'll see what happens next, and how long it will take.