Actually, this is a very common issue with Smoke & Mirror trilogy (V1-3). I can tell from having my hands on multiple sets that brand new, the decks barely fits inside of the boxes, let alone after some usage. Taking out the extra cards should help but then the question is.. where to keep those? Deck pressing (like with the books) does help but not all that much.
Is it actually impossible to get them back in or is it just very tight?