What are the most common irrigation system problems contractors run into?

Age and sun related deterioration.

Shallow lines in a sandy bottom

The most common problems in northern Indiana, i have came across is failure in weatherization.  I usually find several broken lines in systems due to freeze breakage.  The other problem mostly consists of Zone actuator failures. Some of the systems I come across were poorly thought out or installed. At that point there's very little you can do other than to replace the system in its entirety. Weather is usually the biggest factor in failures here.