Bonus points can be given for any number of reasons such as a gesture of good will from the hotel due to an issue you may have experienced at the hotel, they could be also for a promotion at a particular property. The points are added to your rewards account and will be shown as "bonus points".
My monthly "earnings" from my Marriott VISA card (which are substantial) appear as BONUS POINTS (as distinguished from HOTEL STAY points) in my account summary. See, generally, MR Premier VISA - Ka-CHING!!!