It is also too early to tell what regulators will find, and there is no indication of any wrongdoing by the banks.
Wells Fargo executives have downplayed the risks of the bank's own auto loan exposure. Finance chief John Shrewsberry said in July that the credit scores and other measures of the health of its consumer portfolio of auto loans "has improved not only over the last 5 years, but improved meaningfully from pre-crisis levels."
But auto loans can still be risky, and are showing signs of stress. The share of borrowers who are 60 days behind on their auto loan payments rose 7 percent in the second quarter from a year earlier, and the repossession rate rose over 70 percent in the same period, according to Experian Automotive, though both rates are still near historical lows.
Used car prices fell for the fifth consecutive month in October, which hurts the amount of money banks can get from selling cars that they repossess.
Read MoreMore car buyers struggling to make payments
"Every metric is moving in the wrong direction if you're worried about risk, though it's not going so fast that it's alarming," said Colonnade Managing Director Christopher Gillock.
Unlike property, cars tend to depreciate in value over time, a factor that can add to a bank's losses for every loan that goes bad. If the economy slows down and lenders find themselves with large numbers of bad car loans, that selling pressure could hurt the value of the collateral for loans. In a slow economy, auto dealers often slash prices for new cars, hurting used car values even more.
The independent auto finance companies that banks are funding, including Exeter Finance and Westlake Financial Services, tend to cater heavily to subprime borrowers. Nearly 75 percent of auto loans that finance companies made in the second quarter went to subprime borrowers compared with 18.1 percent for banks, according to Experian Automotive.
Wells Fargo has already experienced headaches from lending money to auto finance companies. In April, New York Superintendent of Financial Services Benjamin Lawsky brought a case against auto finance company Condor Capital, which Lawsky accused of keeping millions of dollars of customer rebates for itself.
Wells had extended Condor $261 million of loans under a credit facility around the time Lawsky had moved to shut the company down. Wells sought in court to reclaim that money, but the funds have been tied up for six months while the receiver searches for a lender to refinance or purchase Condors loan portfolio. Wells Fargo has recovered some money, and its current exposure is around $200 million.