If you have skills selected for your character and then change the scenario, it leaves the skills there and gives you you’re points, making it possible to have essentially unlimited skill points. I’d personally say that starting the game with 20 dodge, 20 melee and 20 cutting is a tiny bit game breaking.
I recall merging something to deal with this a while back. That said, I’m also not particularly concerned, as you can turn the chargen points and the -vantage caps (separately) up to 1,000 if you so choose. For some reason points people manage to glitch are (somehow) More Usable than points they just ask for.
So as Kevin put it, congrats on breaking the game, hope you like playing with the pieces.