The scariest part of this single program was that its millions of quotes accounted for 10 percent of the bandwidth that is allowed for trading on any given day, according to Nanex. (The size of the bandwidth pipe is determined by a group made up of the exchanges called the Consolidated Quote System.) (Read More: Cuban, Cooperman: Curb High-Frequency Trading.)

“This is pretty out there to see this affect this many stocks at the same time,” said Hunsader, adding that high-frequency traders are doing anything to “tip the odds in their favor.”

A Senate panel at the end of September sought answers on high-frequency trading, as investigators look into the best way to stop wealth-destroying events such as the Knight Capital Group computer glitch in August and the market “flash crash” two years ago. (Read More: Ex-Insider Calls High-Frequency Trading ‘Cheating’.)

Regulators are trying to see how they can rein in the practice, which accounts for 70 percent of trading each day, without slowing down progress and profits for Wall Street and the U.S. exchanges.

“I feel a tax on order-stuffing is what the markets need at this point,” said David Greenberg of Greenberg Capital. “This will cut down on the number of erroneous bids and offers placed into the market at any given time and should help stabilize the trading environment.”

Hunsader warned that regulators better do something fast, speculating that this single program could have led to something very bad if big news broke, or if a sell-off occurred and one entity was hogging this much of the system.

For the best market insight, catch “Fast Money” each night at 5 p.m. ET, and the “Halftime Report” each afternoon at 12:00 ET on CNBC. Follow @CNBCMelloy on Twitter.











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