Something that's troubling causes you concern or worries you. Your parents might find it troubling if you decide to go to clown school instead of college.
A troubling development for a sports fan might be watching her favorite team lose three games in a row. A patient's troubling cough might spur a doctor to order a chest x-ray. Anything that upsets or disturbs you is troubling. The adjective troubling can be traced back to the Latin word turbidus, "muddy" or "full of confusion."