You set expectations with every action you take.

As soon as you start to put in "a little extra" at no charge, they will come to expect it. Then, when you eventually get frustrated that all your time is being eaten up by "little extras" and demand to be paid, you will potentially disappoint and aggravate your client. It's human nature, and nothing against the client of course.

I try to roll up small changes into larger updates, and if not possible to set a minimum fee for any work performed.

For really big projects, especially projects involving multiple stakeholders (or government contracts, egads), I always require a feature change request form. That way all changes that conflict with the SRS are reviewed, integrated, and added to the invoice.