So, your saying its not really coughing?

Kittens can do this 'clearing their throat thing' where it looks like they are gonna be sick, its actually that while grooming a hair gets stuck at the back of the throat and irritates them and does look like heaving. I am pretty sure that this is what it is, considering you have just been to the vets with them and no cat flu symptoms are present.

Actual 'coughing', usually indicates heart failure or lung disease (both rare in young healthy kittens-more an older cat thing). Which you would have to be really unlucky to be happening with them both.

If you continue to worry about this, call your vets and ask their opinion! Cos you have already been so recently, they will offer free help over the phone. Let them decide if you need to go back with them!