Where do leaks on roofs/shingle start from?

They can start from a number of places. A broken or missing shingle, improper flashing, a hole from something like an antenna being mounted to a roof, Ice dams, etc. The hard part about tracing leaks is that the drip in the house may not be exactly below the source of the leak. Often, water gets under a shingle, and runs down the plywood until it gets to a seam. Hope this helps.