I think that happens when a plant turns into a weed and then a peep plucks the weed for you. Do you have that ordinance called Beautiful Town (or something like that)?

I try to water 2x a day, because I think if you water at 8 am and then the next day real life interferes with gaming until 4 pm, you can lose plants to weeds because they went too long without water.

I really like the irrigation system. Totally worth it.