When customers started complaining early last year about spiking water bills, authorities downplayed the situation. Water department officials repeatedly said that leaky toilets, broken sprinklers and the rising cost of water were likely to blame, even as customer complaints flooded into the agency’s public hotline for months. However, a recent analysis by the San Diego Union-Tribune has shown that single-family homes serviced by the city’s water department were collectively overcharged by more than $2 million last year — with some residents receiving bills for tens of thousands of dollars.