Absolutely agree. You are only required to do what you contracted to do and no more. If they want additional work performed, give them a proposal to perform that work or refer it to another vendor.
Here I'm going to disagree. If all the circuits were operational before you began to do the panel change, then they should be operational afterwards as well. By operational I mean that the breaker held closed. You have no knowledge or obligation to know what's going on with those circuits after they leave the panel beyond properly filling in the index.
In my opinion, if you see a violation in the panel, you have an obligation to correct it. This would include putting a smaller breaker on a circuit if it is oversized for the wire. (But never a larger breaker on an oversized wire since you don't know the downstream wire sizes and equipment needs). If you happen to see a violation outside of the panel (e.g. crawling through the attic), you have an obligation to notify the owner. Then you can (if you want) ask if they want it corrected (at extra cost). You have no obligation to fix it without compensation, however I personally would leave that circuit off if it presented an imminent danger.