If you have a clearly defined scope to begin with, then theoretically a Change Order would be obvious. If something does come up, it would be either you asked for something different to be done or an "unforeseen condition" ie: You are having some siding replaced, they remove it, and found a ton of rot in the sheathing. With a clear scope up front about what is and isn't included, you can refer back to that contract.
If you feel that the Change Order work should have been in the scope of the original contract, say so. If the initial scope is vague or verbal, then you either have to pay it or don't agree and risk the guy walking off of the job. At which point you pay for the work done and bring in another guy to finish it.
One of the other things people run into, and our firm deals with this all of the time, people go for the cheaper bid and end up paying more than our original bid via Change Orders. This is something that can be resolved by calling references of the Subcontractors. Ask for the reference of a job that required Change Orders.
I suppose the biggest thing I can say is define everything up front, do due diligence on the Contractor, sometimes it's worth paying a little more to work with a professional and not some guy with a pick up truck and a Class B License who works on a hand shake. If you do, have a good contract. With all this, Change Orders should not be a problem since they would be obvious.