So what's there fort he traders to be worried about? Maybe they are starting to realize it is all just another engineered problem?

Traders waited nervously Thursday for the Nasdaq to begin trading after its largest intra-day shut in recent memory.

"When everyone comes back online at the same time that's when even more dangerous things can happen in the marketplace," said Sal Arnuk, the co-founder of Themis Trading.

The Wall Street Journal pointed to Apple as a good example of the chaos that could ensue. The tech giant's stock plunged shortly before the Nasdaq glitch.

The Nasdaq earlier halted trading in all securities Thursday until further notice due to a problem affecting quote dissemination.

Dozens of publicly traded companies, including high-profile companies such as Apple (AAPL), Microsoft (MSFT) and Facebook (FB), were showing their shares halted. The Nasdaq status message was time stamped at 12:14:03 ET.

Dow Jones reported at 1:06 pm ET that trading would resume "shortly," though the exact timing was not clear. An average of 1.6 billion shares have been traded on the Nasdaq every day this August, according to statistics from Sander O'Neil.

Despite the freeze, Nasdaq that it will not cancel orders. "Nasdaq will not be canceling open orders on the book. Customers who wish to cancel their orders may do so and any customer who wishes to not participate in the re-opening should cancel their orders prior to the resumption of trading," said a spokesman.

A spokesman for the SEC said, "We are monitoring the situation and are in close contact with the exchanges."

The Nasdaq (NDAQ) options markets also issued a "system update" saying they were recommending firms route all open orders elsewhere.

The New York Stock Exchange said it had halted trading in all Nasdaq securities at its request and was cancelling orders. The NYSE otherwise declined comment. The CME said that it was seeing 'no impact' from Nasdaq's trading halt.

(Read more: 'Knight-mare': Trading Glitches May Just Get Worse )

"You can't trade if you can't get the quotes out," said Rich Repetto of Sandler O'Neill Partners.

"They want everybody else to shut down Tape C trading so they can restart over at the Nasdaq and until they do they can't restart", said CNBC contributor Pete Najarian. Tape C refers to any securities traded over the Nasdaq.

"If I was back in the days of 10 years ago managing 300 traders I'd put the directive out to every one of them 'we don't put any orders in at the open' ... no one trades for 60 minutes," said Joe Terranova, chief market strategist for Virtus Investment Partners and a CNBC contributor.

Despite the quote problem, stocks overall were up in the early afternoon.

The shutdown of exchanges without an external crisis is rare, but a stray squirrel shut down the Nasdaq in 1987, according to the New York Times.
Nasdaq resumes trading after 3-hour shutdown - Yahoo! Finance