Normally the first year there are just juvenile foliage - single needles from stem, no fascicles. Second year you might have a few juvenile needles adjacent to fascicle bundles of 2. P. thunbergii is always averages 2, though it is not unheard of to have an odd occasional 1 or 3, but 99 out of 100 fascicles on the same tree should be just 2.
If after the seedling is 5 or more years old, and it still produces regular 3 needle fascicles, there is a good chance it is not P. thunbergii. On a young seedling I would not worry, as it probably has not "settled" into mature growth.