It happened to me before as well. In my case it was adding japanese stickers to the internal documentation (it was a japan import). The retailer also said that sometimes there's a QC check and they re-seal the box.
In Japan, sometimes Takara opens some MP figures, inspects them and reseals them. Doesn't happen often, but I've seen it before (for example, my MP Clampdown was double-taped, but was brand new otherwise). If it's tied down and everything looks brand new on the inside, I wouldn't think too much into it.