Thousands of people subject to immediate deportation have also been charged with the misdemeanor offense of trespassing on military property.

The move is raising questions about using military-designated land for civilian enforcement and how agencies coordinate across federal lines.

Federal prosecutors, who can face discipline for not advancing the Trump administration’s priorities, are bringing military trespassing charges against immigrants with little evidence.

Along the Southwest border, federal courts have been jammed as prosecutors tack misdemeanor military-trespass charges onto thousands of illegal-entry cases. The extra counts have clogged dockets for ...