(Read more: Nasdaq closes 1% higher after 'Flash Freeze')
"The negative impact is going to be felt tomorrow," said Todd Schoenberger, managing director at LandColt Capital. "Obviously this technology is failing. The lack of transparency—we haven't heard from the Nasdaq, we haven't heard from Washington—it creates chaos and uncertainty.
"You're going to have investors thinking, 'This is the Wild, Wild West and I don't want to be in this market.' "
(Read more: Cramer: We need a disaster plan, now!)
After the day's tumult, officials tried to sort through what happened and make some sense before Friday trading opened.
Nasdaq officials cited a "connectivity issue between an exchange participant and the SIP," or Securities Information Processor. It did not name the specific firm involved.
"NASDAQ OMX will work with other exchanges that are members of the SIP to investigate the issues of today, and we will support any necessary steps to enhance the platform," Nasdaq said in a statement.
August has had a recent history of trading issues, as the Knight Capital trading debacle happened in 2012 and Goldman Sachs just had its own mishap.
(Read more: Goldman trading glitch could cost over $100 million)
That works in the market's favor, though, with several traders saying the low market volume helped minimize damage caused by the Nasdaq shuttering.
"This is a lot less serious on a Thursday afternoon in August than it would be at some other time," said an investor with regulatory experience who asked not to be named.
"It will affect people who really need liquidity and were planning to get it from Nasdaq stocks. These things happen nowadays, markets break down, it's an assumed risk of trading that the market you need to trade in could break down."
—By CNBC's Jeff Cox. Follow him
@JeffCoxCNBCcom on Twitter. CNBC's Margaret Popper contributed to this report.