Since your opponent already threw his dice, he definitely forefitted his opportunity to transfer tokens. It's a bummer that he only realized he had forgotten to transfer focuses before he saw two eyes staring up at him, but it's more his responsibility to remember to do that and not yours.
I strongly fall in favor of playing in a more deliberate manner, asking the opponent if they're ready to start flipping dials, rolling, etc (I typically ask if they want to make any modifications every opportunity they have to do so, it's quick, easy, and unobtrusive - sometimes even cooperative) - but if you run ahead of them and they've still got actions they should have access to, the reasonable thing to say is that they can still trigger/activate whatever so long as they don't take any steps themselves to progress the game past a point that would deny their own window - and even that exists in a very situational place as it's a concession open to abuse.