This is a very good question!

Excessive irrigation can leach elements from the soil, and can cause root systems to grow closer to the surface of the soil (where there is more air). Depending upon the drainage capacity of the soil, excessive irrigation can cause oxygen depletion, can harm essential microorganisms while fostering the growth of pathogens. Such conditions create stress for plants, ultimately resulting in plant decline, disease infection, and even insect infestation.

There are many ways for irrigation systems to be set up incorrectly. The most common is to set the clock to come on for 10 to 15 minutes at each station, three times a week (or similar). This also encourages very shallow and limited root systems, very prone to damage from freezing temperatures and/or hot summers.

At the very least, turf and landscaping should be set on entirely separate stations. Lawns will always need more frequent watering than landscape ornamentals, for example. Woody plants, when properly weaned from frequent, shallow watering cycles rarely need watering at all. And do much better because of it.

In all of my many years as a consultant, more problems have been caused by the use of irrigation systems than (almost) anything else. Consequently, we are one of the few properties without irrigation, yet can boast about flourishing planting beds, large perennial gardens, healthy new trees, and lush grass.

GW's Irrigation Forum is fairly active with informed contributions.