Travel reimbursement and "bonus programs" 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.)
Unless the funder has a specific policy (which they should tell you about), common practice is that "reward points" (including frequent flyer miles, etc) are yours to keep, and don't deduct from your reimbursement.

You're right that there is something a little shady about this, but basically, nobody has figured out a better way to handle it, and travelers are used to keeping their points and would get mad if they weren't allowed to.