It's common for SMALL hotels, which don't have night-staff. Some allow it if you ASK THEM in advance (e.g.
- Alegria http://www.priceline.com/hotel-alegria-bruges-west-vlaanderen-2411149-hd.hotel-reviews-hotel-guides
- Memling http://www.booking.com/hotel/be/memling.en-gb.html
- Jacobs: http://trips.lastminute.com/vg1/vacanze/hotelsearch.action?idHotel=1001017171&idProvider=108&accomodationOnly=true)
In some cases, extra charges apply because they have to pay someone specifically to wait up for you e.g. Hotel Marcel - formerly Nicolas - http://www.booking.com/hotel/be/nicolas.en-gb.html).
Others allow check-in till 23:30 anyway, e.g. this centrally-located b&b: http://www.booking.com/hotel/be/bb-in-bruges.en-gb.html
On the other hand, late arrival is fine with a larger hotel, especially those belonging to a chain, e.g. Best Western (Hotel Acacia), NH (although I think NH Brugge may be further out from the centre than you want) and Novotel Brugge Centrum (http://www.novotel.com/gb/hotel-1033-novotel-brugge-centrum/index.shtml). And of course the more expensive hotels like Die Swaene.
The Academie is also a possibility: https://www.quickbeds.com/internationalhotel.aspx?propertyid=215477 as is the Rosenburg http://www.booking.com/hotel/be/rosenburg.en-gb.html
I didn't check prices as these may vary depending on the exact date and type of room you want to book.