My 2002 Octavia says "stop brake fault". My inspection (MOT) said my brake drums were bad and the handbrake. I just want to be sure that this is not the front brakes, they should be good. Why does it indicate this "Stop brake fault" 

The drums (where fitted) and handbrake are on the back wheels.

 

I'm not aware of a "stop brake fault" warning on the Octavia. There is a "handbrake on" warning which means that the lever isn't right down, a "brake pad wear" warning which only actually covers the LH inside pad (RHD cars) and an "ABS fault" warning which means that the anti-lock system won't work, but the brakes themselves are fine.