Missed student health appointments: Many schools charge for missed appointments with health services. It pays to call ahead.
Degree candidacy / degree processing / thesis and dissertation filing: These fees generally apply to graduate students, although special undergraduate programs may charge them as well.
Returned checks: Don't bounce checks to your school! Not only will your bank charge you, the school may also charge you as much as $60.
Dorm damage: Just like a landlord, your school reserves the right to bill you for wear and tear to its housing facilities for anything ranging from broken fixtures to adhesive tape left on the walls.
How can you get advance warning of these hidden costs? Some fees are automatic — practically every school will charge you for late tuition payments, card replacements and returned checks. Your best bet for dealing with these sorts of fees is to call the appropriate office in advance and explain your special case (e.g. if you need a replacement card because your wallet was stolen). Many offices will make allowances for extenuating circumstances.
To find out more about course material fees, try calling the department offering the courses. You will probably still have to pay the added fees, but you'll at least get some advance warning so you can adjust your budget accordingly. You might also be able to get some of the necessary materials at a discount or secondhand.
For general service and official document fees, call either your registrar's office or your bursar's office to request a complete list of fees.