It's likely that something either happened to this body and it was pulled off the line (or something), or perhaps there was some lag with LS-6 blocks and they all had this issue.
Never happened. Once a body was started, it was built to completion. There's absolutely no room in an assembly plant to set aside a body for a while and it would cause ripple effects throughout the assembly process.
Another likely scenario would be that the engine and VIN were swapped by a previous owner but not the body tag..... That would explain why the engine and VIN match and just not the tag. I would be looking for the other hidden VINs on that body.