I use a "bonus program" for train tickets, which (allows me to buy tickets with lower fares and) provides for each ticket some "points" which are worth around 2% of the ticket value. I make use of this also when I travel for academic purposes (otherwise the funders would need to reimburse a higher amount). However, for each reimbursement I feel the moral obligation to explain that in some sense I actually paid less for the ticket than what is on the receipt.

How should I deal with this situation? Is there a common practice regarding this? (I guess some institutions may have official policies regarding such situations because many people who are traveling often take part in such programs.)