Penn filed for separation in Marin County last month, but records show he moved to dismiss that filing. The record does not indicate why.
Penn told the New York Daily News that the filing was "an arrogant mistake."
The couple have had an on-off relationship. They filed for divorce in December 2007 but dismissed that petition several months later.
In February they attended the Academy Awards together, but the 48-year-old actor neglected to thank his wife after winning for his role in the drama "Milk."
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