I've got the same situation about the level up. My main character got one point but my secondary character got two points.
I can't remember for certain, but while customizing my character I'm pretty sure that I read one of the skills, traits or whatever that I was thinking about choosing gave more points on level up.
I don't recall if I chose that one or not, but I'd guess that I did since she got 2 points instead of one on level up.
As far as the other points you received with no armor on, I'm not sure.
