The mistake was not spelling out in the contract how much additonal
soffit venting was to be installed, what type, where it would go, etc.
But it did say that sufficient venting was to be supplied as part of
the deal and that any additional work requiring payment was to be
spelled out upfront. The contractor did not ask for payment upfront,
nor does it sound like he asked for it when you called him back over
the soffits. So, I would simply send him a letter spelling out your
position, and indicating that you believe he has been paid in full.

As someone else pointed out, he's unlikely to sue you over this small
amount and if he does it will likely be in small claims court.