After doing the 1st Kishinden quest I gained a lvl I went to spend the points i had 16 points available 12 from lvling up since I didn't spend them on the previous lvl up but where did the other 4 come from? because of them I have 1 point unspent I don't like being unable to spend stat points.

Being unable to spend a point here or there for every level up will be inevitable in time.
And you get 4 extra skill points for completing the Kishinden quest if I recall