Invesco PowerShares Capital Management had 11 ETFs affected by the glitch, a spokeswoman said.
In a letter to clients, BNY Mellon said, "We recognize the trust that you have placed in us, and sincerely regret the disruption this has caused you and your organization."
New York-based BNY Mellon has been under fire from some hedge fund investors for having too many employees and not reining in expenses. The bank has nearly $30 trillion in assets under custody and administration. Smooth fund accounting is something its clients rely on.
Its archrival, State Street Corp is considered the No. 1 provider of mutual fund accounting services.
BNY Mellon spokesman Kevin Heine said he did not know how many funds had been affected.
In addition to Federated Investors, Guggenheim Investments and First Trust Advisors both had ETFs affected by the glitch, the firms said.
"The SunGard system became available with limited capacity late yesterday," Heine said on Wednesday. "Our teams have been working together to clear the backlog and we are working with SunGard to resume normal processing as soon as possible."
BNY Mellon said it was able to construct Monday net asset values (NAVs) for all affected funds. But there remains a backlog of Tuesday NAVs that still need to be generated.
First Trust, which manages several exchange-traded funds, said on Wednesday in a statement that the net asset value of some of its funds contained errors greater than 1 percent.
"The errors resulted from a technical malfunction at our third party administrator, the Bank of New York Mellon," First Trust said.