In practice, however, a more lenient law has long governed the way immigration authorities treat foreigners who marry American citizens: Even if they overstayed, as long as they originally entered the country legally, they had been allowed to “adjust” their status to permanent resident.

Mr. van Sander, whose original paperwork would have stopped the 90-day clock if it had not been flawed, seemed to be on track for such an adjustment in March, when the couple refiled all the papers on the advice of an immigration officer.

But on April 22, a decision by the United States Court of Appeals for the Third Circuit in a separate case changed the legal landscape for such couples in New Jersey, Pennsylvania, Delaware and the Virgin Islands. Lawyers say the van Sanders are among thousands of couples who could be adversely affected by the decision, which leaves the foreign spouses no defense against deportation if immigration authorities, at their discretion, decide to expel them.

The decision echoes and sharpens recent rulings in 6 of the 12 regional circuits across the country (but not the one that covers New York), holding that after a 90-day stay, foreigners who enter the country under the visa-waiver program cannot fight summary deportation based on their marriages to American citizens.

“It’s surreal,” said Ms. van Sander, who went to immigration court with the Princeton chaplain and a lawyer on Tuesday to plead for her husband’s release. The judge told them that the appeals court’s decision left her no jurisdiction over Mr. van Sander, and that he was not entitled to a bail hearing.