Raneta Lawson Mack of Nebraska said the double billing drained her account.
"They even went as far as to pull money from my line of credit to cover their error of double debiting," Mack said.
The glitch at Wells Fargo's system was a "communication error" and disrupted only the online records displayed to customers, spokeswoman Wendy Grover said. In reality, she said, the bank debited the correct amount for each of its customers' bills, and the incorrect amount never left their accounts.
She said most of the customers affected were located in the Midwest but that the bank was unaware of the exact number.
As for Mack's allegation that Wells Fargo drew money from her credit line, Grover said that information was also an erroneous message from the bank's system. Her credit line was left untouched, Grover said.
Wells Fargo launched its Web bill payment service four years ago but has seen the number of competitors rise dramatically over the last two years. Among the crop of companies vying to pay bills for consumers via the Net are Bank of America, CheckFree and Paytrust, which acquired rival PayMyBills.com this week.
Analysts and many executives have said proving that paying bills online is secure and accurate is paramount to drawing in the public, which has thus far shown a lukewarm response.
"We feel that the problem is fixed and that it shouldn't happen again," Grover said.