The appeals court this week acknowledged that the government “violated the Fourth Amendment” when F.B.I. agents sought and obtained, without a warrant, Mr. Carpenter’s location data. But under the good-faith exception to violations of the Fourth Amendment, the court said the agents acted reasonably and in “good faith” — and so whatever they gathered could still be used at trial. The F.B.I. merely followed the law and the rules that applied at the time of the violation.

The A.C.L.U.’s Nathan Wessler, who argued and won the Carpenter case before the Supreme Court, wrote in an email that the decision this week is “a terrible injustice” for his client. “In the digital age, when an incredible volume of our most sensitive information is vulnerable to unwarranted snooping by police, it is crucial that people have a meaningful remedy for violations of their rights.”

Mr. Carpenter’s loss in the lower courts was not unexpected. Still, the good-faith exception, which the Supreme Court last upheld in 2011, appears counterintuitive — if not wildly unjust.

Orin Kerr, a Fourth Amendment expert who has unsuccessfully challenged the good-faith exception before the Supreme Court, reasoned that broader Fourth Amendment protections for everyone at the expense of relief for people like Mr. Carpenter may be a bargain the justices can live with. The justices, after all, are human and may feel more comfortable ruling for expanded civil liberties, so long as they don’t also have to let the bad guy go free. Still, the current system is far from just. “Supreme Court cases should mean something,” Mr. Kerr said in an email. “The Supreme Court is supposed to decide a person’s case, not just settle the rules for everyone else.”

Mr. Wessler, who is challenging the adoption of a good-faith exception in a case in Georgia — one of several states that don’t have good-faith exceptions to the Fourth Amendment — said the development of the law may suffer in the long term, as lower courts excuse violations while refusing to expand privacy rights.

“When courts dodge the Fourth Amendment question and rule just on good faith, it leaves the public and police without clear guidance about what the Fourth Amendment means and how it should apply to novel but important digital-age intrusions,” Mr. Wessler wrote in an email.