Nick Spicer, Al Jazeera's correspondent in Philadelphia, said: "The first hour of the debate was spent defusing these two controversies, it was an hour before they were asked any questions about the economy, which is the number one issue for voters here."
The televised debate on Wednesday was their first in seven weeks and the last before the Pennsylvania primary next week, which Clinton is expected to win.
However, her lead in state opinion polls has been dwindling and she needs a decisive victory to help her close the gap in both the popular vote and the pledged delegates who pick the nominee. 'Properly phrased'
Obama said he had made a mess of remarks describing the mood of residents of small towns who are struggling due to the economy.
"The problem that we have in our politics, which is fairly typical, is that you take one person's statement, if it's not properly phrased, and you just beat it to death, and that's what Senator Clinton's been doing," Obama said.
Clinton launched a television advertisment in Pennsylvania saying that his comments were "a fundamental misunderstanding of religion and faith".
She warned the remarks would hurt Democrats if Obama won the nomination to face John McCain, the presumptive Republican nominee, in November's presidential election.
"Obviously, what we have to do as Democrats, is make sure we get enough votes to win in November," she said.
"The Republicans, who are pretty shrewd about what it takes to win, certainly did jump on the comments."
However, she said that her rival would be able to win the White House if he were to become the nominee.
Asked a similar question about Clinton, Obama said: "Absolutely and I've said so before".
Clinton has previously declined to make a similar statement about him.
There seemed to be little in-depth debate of issues, but both senators did promise to defend Israel against any Iranian attack.
Obama renewed a promise of "direct talks" at a leaders' level with Tehran, while Clinton ruled out any summit talks but backed low-level diplomatic engagement.
"An attack on Israel would incur massive retaliation by the United States," Clinton said.
While Obama said: "The US would take appropriate action."