There are various ways of doing that.

• You can specify this in the Expense Note at the expense line level, or in a chatter note of the expense document.
• You can use analytic accounts (at the line level) to categorize different type of expenses. One of them could be "non-refundable".
• You can decide that an expense sheet that is in the "Approved" stage should not be paid and that the ones that are in the "Waiting Payment" stage should be paid.