I'm gonna go against the grain and say to do absolutely nothing in game. Ever. Worst case scenario, this encourages more fudged dice rolls, but with just more care that he's not caught. It also has the potential to foster a real "us vs the GM" environment (even if it's just one player who feels that way), which is something you clearly don't want.
Always handle out of game things (mechanics, character balance, attitude) entirely out of game.
Check that it wasn't accidental - we've all been guilty of making mistakes, especially when we were new players (and especially with a new system - if he hasn't played FC before). When 2.0 was new I spent an entire session thinking Surge of Speed was at will because I built my character quickly (and somehow missed half the text). I've also made math errors, or mistaken things as applying when they shouldn't - we all fuck up from time to time. Could have been just an innocent mistake that he made because he's unfamiliar with the game / group. Punishing someone for "Ok... I need to make this, so what are all my modifiers to the roll? "X + Y + Z + oh yeah X" as a legitimate mistake is pretty unfair. Which from your posts, you certainly don't seem to be. It's easy to be a little nervous and accidental add something twice. I've done it before (usually from sleep deprivation, rather then nerves or whatnot), and I'm sure even those calling for him to be penalised have too.
If it was intentional, and to save the scene - make sure he knows that Action Dice exist for the express purposes of doing that (again - especially if he's new(ish) to FC/SC). Show him the Cheat Death rules so he doesn't get worried about losing a character.
Do all of that alone with him, before a game starts / after it's finished. Otherwise it's the whole table vs him, which is extremely uncool. Just emphasise that it's not a big deal - especially if it was innocent - just to take a bit of care, and not worry about the outcome, since the game has plenty of rules in place to fudge things legitimately. But no penalties - they'll just alienate the kid, which is clearly something you don't want.