A full wet block would be best for a small square, but I can't say whether it will be enough to stretch it out to 12 inches. It might though, maybe the pattern for that square just needs a good blocking? Some patterns like mesh or weaves tend to shrink up from knitting, but are meant to be blocked well to open the pattern up.
When you assemble the blanket, the mere act of seaming them together will help greatly with their measurements. If the small square blocks easily to 12 inches, I wouldn't worry at all. But if you have to struggle to get it to 12 inches while blocking, I would re knit it with a larger needle. It's not uncommon for the separate blocks in an afghan to have totally different gauges from each other even though they use the same yarn.