The brown case is normal. Stores often just put a guitar in whatever case they have in the back that fits and says Fender. This was very typical back in the 50s and 60s, so it's quite possible it was just put in an older case and everyone went on their way.
Hell, even ten years ago. I bought an AVRI Jazzmaster and out came an AVRI case, but for a Strat. Obviously I didn't take that case because the Jazzmaster doesn't fit a Strat case. But in other cases (no pun intended), It happens. Sometimes they just grab whatever looks suitable.