Doxo promises to provide secure payments, tracking, custom reminders and mobile services for customers with linked bank accounts, and the FTC indicated its concern about the company lies in the way it represents its role relative to billing entities.

"Doxo intercepted consumers trying to reach their billers and tricked them into paying millions of dollars in junk fees," Samuel Levin, director of the FTC's Bureau of Consumer Protection,  said in line with the complaint alleging violations of the Gramm-Leach-Bliley Act and other rules.

The company indicated that it plans to fight the complaint "on behalf of all consumers and billers who deserve a better bill pay experience," calling the FTC's action "inaccurate, and unjust," and reflecting "a fundamental misunderstanding of the existing bill-pay market."

While the complaint references issues with "car loans, utilities and medical bills," there have also been signs of confusion about its mortgage payments. It also follows closely on the heels of a separate Consumer Financial Protection Bureau report about servicing fees, and reflects growing regulatory tension over certain charges for payment services.

Doxo lists bill payment services for various mortgage firms on its website, but also notes it "is not an affiliate of or endorsed by" any of the businesses.

At least one mortgage servicer has had a clarifying alert about Doxo posted on its website that advises borrowers not to remit payments through the vendor.

"BSI Financial Services does not accept credit/debit card payments and this company is not affiliated," the company said in an online notice.

The FTC filed its complaint in the Western District of Washington, where Doxo is headquartered.