It is unknown how many Wells Fargo customers were impacted.
Wells Fargo said workers discovered the problem following routine maintenance.
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"We apologize to our customers who may be experiencing an issue with our online banking and mobile app," Wells Fargo tweeted.
The company said late on Thursday that it had restored ATM access and some online features, but that that other features, such as credit card and mortgage balances, were still being worked on.
"We continue to work on restoring all our services as soon as possible, and encourage customers to contact us if they have questions or concerns," the latest update reads.
On Friday, Wells Fargo told ABC that some customers were experiencing an issue with direct deposits on Friday morning. The company issued the following statement:
"As a result of the process to restore systems yesterday, some transactions and balances were not reflected in online banking or ATMs earlier today. The transactions were processed normally, and customers and team members can use their accounts with confidence."
When customers logged in on Thursday, some saw a message that apologized and said mobile banking was temporarily unavailable.
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"I got on my Wells Fargo App this morning to see what kind of funds I had to take them out, and it wouldn't let me log on or do anything," said Jonas Palmer.
"It is sort of messed up and you can't see what your account balance is, but I could at least deposit a check," said Garth Connor. "I am a government worker who went through all the shutdown stuff and so my bank balance is different than it normally is."
Late Thursday, the company promised on Twitter that customers would not be responsible for fees resulting from the outage.
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San Francisco-based Wells Fargo, the nation's third-largest bank, can't seem to catch a break when it comes to its customer service issues over the last few years. The bank has been plagued with scandals over its sales practices, attaching insurance contracts to auto loans that did not need it, and putting homes into foreclosure where it shouldn't have happened. The bank has been fined more than a billion dollars for its customer service failures.
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The Associated Press contributed to this report.