That would be my guess, since otherwise the system is bugged. And I haven't heard of anyone complaining about any weird situations where a valid unused code couldn't be redeemed.
Also, it seems that for multi-obtainable events, it doesn't actually store the WC ID in the internal received list at all in most cases. I just opened up a couple of my JPN saves, and neither WC 0137 (VC Mew) nor WC 0161 (JPN movie Volcanion) are listed in the received list, even though their used wondercards are still on the save. Interestingly though, 0095 (Hiroshima Magikarp) is on the received list, even though it was also multi obtainable. Maybe because it isn't a code? (disregard, I forgot I was testing something on that save)