This should have been discussed before the Stay. There are two things to keep in mind:
#1- your rates should be set high enough to cover incidentals usual to the care and supervision of your guests. This is why Sitters set their own individual rates and what pet parents assume they are paying for.
2- pet parents should be informed of what their pets need to bring with them (if staying at the Sitter's), or have supplied in their homes (if Sitter is House Sitting ), prior to their stay.
Typically, the pet parents should provide their own food, regardless of where the care is occurring. The simple reason is that every dog will have a different diet and otherwise, you, the Sitter, will end up with tons of half-used bags of food and a lot of out-of-pocket expense.
Puppy pads are your call. Many Sitters charge more for puppies because of the extra work / expense, in which case, you would have charged up front in your Puppy Booking rate.
If the dog were misrepresented, such as stated that he was potty trained but wasn't, and you had a lot of surprise expenses due to the pet parents lack of disclosure, then you may choose to ask them to reimburse you or just walk away in lieu of a good review and lesson learned.