Many things can cause noise on the line, but most of the truly annoying types are caused by electrical problems, such as bad AC power, which causes a hum or popping & ticks caused by grounding issues. This will probably be persistent, but might not affect all users. Also, do not rule out that this issue could be sound coming from the other end and being amplified along the way. The frequency of occurrence will help you figure this out.
The best way to resolve this is to correlate the incidences of noise with specific routes or pieces of equipment. Check power cables, Ethernet cables and all grounding. Check all the way down to the handset. This can easily be confused with clipping depending on timing of the clip; often the User will describe this as "Static."
Also make sure that an unshielded (older models) cell phone or speaker is not sitting next to the phone or its wires.