Salaat First is the second app in two months that has come under criticism for sharing user data belonging to Muslims with US contractors who are linked to the US security establishment.
Acting head of US Customs and Border Protection John Sanders announced his resignation amid an outcry over alarming detention conditions of migrant children in Texas and heat-induced deaths of immigrants in border states.
Thousands of migrants are seeking to apply for asylum in the United States at the border town. As their fate remains uncertain, some say they are willing to settle down in Mexico, while others are determined to move on.
The United States has halted all border traffic at the busy crossing between San Diego and Tijuana, Mexico to prevent migrants from crossing border.
The two-hour glitch was fixed about 0230 GMT (9:30pm EST). The Customs and Border Protection agency said there was no indication the service disruption was malicious in nature.
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