If so, it could have a significant effect on consumers' wallets. Overdraft fees account for the vast majority of the fees consumers pay on their checking accounts. Consumers who opt in to overdraft protection pay an average of $21.61 monthly in overdraft fees, or more than $250 annually, compared to $2.98 monthly and less than $36 annually for other consumers, according to research by the bureau. The fees account for 75 percent of total checking account fees for consumers who opt in. Younger consumers are especially vulnerable to being hit with high fees.
Read MoreATM, overdraft fees surge
Not surprisingly, overdraft fees also represent a meaningful revenue source for banks. Before the bureau's rule changes, in 2009 banks took in about $37.1 billion from overdraft fees, according to Moebs Services, an economic research firm. That dropped to $31.6 billion in 2011 after the opt-in rule took effect, but then inched back up, and in 2014 stood at $31.8 billion.
Regions is not the first bank to run into trouble on overdraft fees. They have been the subject of litigation for several years, and big banks like Bank of America and JPMorgan Chase have paid hundreds of millions of dollars to settle claims.
Even so, many consumers remain confused about overdraft rules. In a survey by the Pew Charitable Trusts, some 52 percent of respondents did not recall opting into overdraft protection but were still charged a fee in the past year.
Read MoreConfusion still surrounds overdraft rules
The good news is that it is easier than ever for consumers to protect themselves from overdraft fees. For starters, small banks and credit unions generally charge much lower fees, according to Michael Moebs, economist and CEO of Moebs Services.
"The best deal in banking services is a community bank or credit union," he said. While overdraft fees industrywide have held steady for the past two years at around $30, he said, the smaller institutions' fees typically run around $25, compared to roughly $35 at many big banks.
Greg McBride, chief financial analyst at Bankrate, also said credit unions in particular tend to have lower fees. But, he added, consumers would do best to simply avoid incurring the fees in the first place.
Read MoreHow to avoid the bite of big bank fees
"If you are shopping around on the basis of overdraft fees, I think that signifies a greater problem," he said.
Consumers can easily avoid overdraft fees by taking a few simple steps, McBride said. First, it's a good idea to link your checking account to your savings account. That way, if you run short, your own money will cover the difference and your bank will probably only charge a nominal fee.
You can also sign up for email alerts that will let you know if your account balance is below some preset amount.
Even without those things, McBride said, just paying attention to your account balance has never been easier. "With 24/7 online and mobile account access, there is really no excuse for not having a handle on what your available balance is."