NEW YORK—Wall Street ended a whipsaw day mostly lower, as fears of escalating instability in the financial sector kept investors on edge despite a steep retreat in oil. The Dow Jones industrials on Tuesday had their first close below 11,000 since July 2006.

Just days after the government said it would aid Fannie Mae and Freddie Mac if necessary, Federal Reserve Chairman Ben Bernanke told Congress the U.S. economy faces “numerous difficulties.” During the day’s testimony, Treasury Secretary Henry Paulson also said the Bush administration has no immediate plans to lend money to the m...