Moody's cut Greece's bond ratings by another notch into junk status. In addition to the increased risk of restructuring, the agency cited "highly uncertain" growth prospects and missed targets in budget reforms.
Financials led the markets lower, with the KBW Bank Index sinking to a six-month low and below its 200-day moving average, following more dismal news on the housing market Tuesday when the S&P/Case-Shiller home price index showed home prices fell to a new recession low in the first quarter.
Banks are exposed to the housing market not only through their loan portfolios, but also through holdings of mortgage-backed securities. (Read More: Mortgages Still Cloud Bank of America Outlook)
In further bad news for the housing market, the Mortgage Bankers Association reported its index ofmortgage applications fellalmost 4 percent last week, led by refinancings, which fell 5.7 percent.
General Motors, Ford and Toyota slipped after the automakers posted figures that showed a decline in May auto sales. In addition, Toyota said it is recalling 105,000 early models of the Priusbecause of problems with power steering and the gearbox.
Nokia declined for a second day to a 13-year low after at least eight brokerages cut their price target on the stock. The mobile phone handset maker cut its sales outlookTuesdayand said it expects sales from its products and services to be far worse than initial projections. Research In Motion also slippedamid worries the Blackberry maker could be in a similar situation.
Juniper plunged after the CEO said the firm may see a negative impact from the Japanese earthquake and added that the company is not immune to reduced federal spending.
Meanwhile, Expedia shares said it is partnering with deal-of-the-day site Groupon to create a new discount service.
Also on the tech front, Yahoo slumped despite news the search-engine company said it resolved a dispute with partner Alibaba Group over the Chinese company's transfer of its prized online payments unit.
Among retailers, Macy's slipped even after the department-store chain reported a 7.4 percent gain in May sales, beating the 5.6 percent gain expected by analysts. Most retail outlets are reporting same store sales on Thursday.
Dollar General sank after the discount retailer's earnings fell short of expectationsas it needed to cut prices on clothes. And Tiffany's also sagged after Deutche Bank downgradedthe luxury retailer to "hold" from "buy."
Lions Gate Entertainment jumped after the entertainment company beat earnings expectations, helped by lower distribution and marketing costs. Revenues, however, fell short.
On the M&A front, KKR said it was selling the principal subsidiary of Hilcorp Resources for $3.5 billion to Marathon Oil. The deal is for 140,000 acres in the Eagle Ford shale field in South Texas.
Sealed Air slipped following news the Bubble Wrap maker will buy Diversey Holdings, a private cleaning product company, for $2.9 billion in cash and stock.
The dollar rose against a basket of currencies. Meanwhile, oil prices declined. U.S. light, sweet crude fell $2.41 to settle at $100.29 a barrel, while LondonBrent crude slipped $2.20 to settle at $114.53 per barrel.
Precious metals closed mixed. Gold rose 0.4 percent to settle at $1,542, while silver fell 1.6 percent to $37.69.
On the economic front, the Institute for Supply Management's index of manufacturing fell to 53.5 in May from 60.4 in April, the lowest level since September 2009. Analysts expected the index to fall to 57.7.
Construction spending, meanwhile, rose 0.4 percent in April, the Commerce Department reported. But spending in April was revised down to a 0.1 percent gain from the previously reported 1.4 percent gain. Economists surveyed by Reuters had expected construction spending to rise 0.3 percent.
And the private sector added only 38,000 jobs in May, according to a jobs report from Automatic Data Processing and Macroeconomic Advisers, far less than what most analysts had expected. In April, the private sector had gained 177,000 jobs, down from the 179,000 initially reported.
The weak economic news is prompting analysts to cut their forecasts for April non-farm payrolls, which will be released on Friday. Goldman Sachs cut its forecast to a 100,000 gain from 150,000, while Credit Suisse cut its forecast to 120,000 from 185,000.
Economists surveyed by Reuters had expected payrolls to rise by 180,000 in May, down from a gain of 244,000 in April.
Another report showed the planned layoffs rose 37,135 job cuts last month, up 1.8 percent from April, and up 4.3 percent from a year ago, according to Challenger, Gray & Christmas, an outplacement firm.
Wednesday's weak economic data continues a recent trend and the “negative seasonality factor” will likely keep the markets choppy for the “next few months,” said Ryan Detrick, senior technical strategist at Schaeffer’s Investment Research.
However, Detrick said a lot of the economic concerns have already been priced into the markets and he expects stocks to climb in the second half of the year.
In Europe, stocksclosed lower amid renewed worries over Greece's debt troubles. Moody's Investors Service downgraded Greece again and said it sees "at least even" chance of a default.
On Tap This Week:
THURSDAY: Chain store sales, jobless claims, factory orders, natural gas inventories, oil inventories, money supply.
FRIDAY: Non-farm payroll report, ISM non-manufacturing index; Wal-Mart shareholder meeting.
More on CNBC.com