Oh yeah, it seems that I see it more and more lately, but we also use a lot more vinyl than we used to. Even 3M has issues with partially punched holes sometimes, we never use Oracal here. I'd assume that the blades(?) on the punches wear out eventually and need sharpened or replaced and that is when we see this. We've been trying to find a punching machine for sale so we could convert our own vinyl, but haven't found one yet.
About once or twice a year we will get a bad batch that is punched incorrectly (not even sure how that happens) and it'll not run right on the sprockets and jump off every time. Thankfully Grimco takes care of these issues quickly for us.