Just played a game where I used rebuttal on a falling star and took control of it. They then used not so fast on the falling star. Not so fast states an enemy spell, can he not so fast the falling star as its not my spell ... im just making new choices for his spell..

No — but not because of control. Rebuttal genuinely does change who controls that spell: once it resolves, the Falling Star is your spell, it's still owned/trash-bound to him, and it counts as an enemy spell relative to him (FAQ 1152). So "you're just making new choices for his spell" isn't the reason it fails.

It fails because Not So Fast needs the spell to choose a friendly unit or gear, and Falling Star doesn't choose anything while it's on the chain — its two damage instances aren't aimed until it resolves and creates the reflexive triggers (FAQ 1644). So Not So Fast can't counter the Falling Star spell itself at all.

What he can do is counter one of the two reflexive triggers after Falling Star resolves, since those do target — and because you control the Falling Star, those triggers are yours to aim, so he can only stop one 3-damage instance, not both.