No house is perfect. Even the best built and best maintained homes will have a few items in less than perfect condition. Below are some items found when inspecting a home:

Floor Framing/Structure Inadequate ventilation and the damaging effects caused by it are the most common and reported defects.

Roofing Problems with roofing material are common. Usually it doesn't mean the roof needs replaced, simply that it is in need of maintenance or repair. Missing flashings in key locations can lead to moisture infiltration and damage to the building exterior and more.

Ceiling stains Past or current leaks are common. A moisture meter is essential to the inspector when determining prior or active leakage.

Electrical hazards Most common in older homes, but often found in newer homes as well. Electrical hazards come in many forms, from ungrounded outlets to wiring done incorrectly by the homeowner.

Wood rot Is due to moisture over an extended period of time. Most commonly found around tubs, showers, toilets, roof eaves, exterior trim, and the floor framing/structure. 

Water heater installations Improper/inadequate venting of the gas appliance is a serious safety concern.

Gas furnace Most gas furnaces seem to be in need of routine maintenance.  Some are old enough to pose a safety hazard to the occupants.

Plumbing defects Plumbing issues commonly found include dripping faucets, leaking fixtures, slow drains etc... Even in brand new homes, it is common to identify plumbing defects.