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The army does do exercises in aircraft with little or no running lights. This page on Wikipedia has more information:

Black helicopters - Wikipedia, the free encyclopedia

The following are facts and explanations provided by various organizations and experts, including government agencies, regarding the alleged black helicopters:

* At least some sightings of black helicopters are very likely to have been helicopters on exercises and/or missions. The American military does in fact operate helicopters painted in black or dark colors, particularly the Pave Low which is optimized for long-range stealthy insertion and extraction of personnel, including combat search and rescue.

* U.S. Army and National Guard helicopters painted olive drab will appear to be really black in the reddish light of dawn or dusk, or under other low light conditions during the day when their shadow side is viewed against the sky with the naked eye.

* Real black helicopters do exist. Some of them are flown by units of the Army National Guard and are actually black (not dark olive or chocolate brown) when seen in ordinary light. The Department of Homeland Security operates at least one black-and-gold blackhawk.

* The U.S. Army regularly conducts both exercises and operational missions in American airspace. Some of these exercises have taken place in densely populated areas, including Los Angeles, Detroit, San Francisco, Oakland and Washington, D.C. Most operational missions are tasked in narcotics interdiction in the American Southwest and out of Florida. By extensive use of GPS and night vision devices, as well as other classified means, they are able to fly in zero visibility conditions with no running lights. At this high intensity level of operation, training is necessarily almost as dangerous to pilots, other air traffic, and the public as actual combat. Frequent practice is necessary to retain proficiency.

* Many defense contractors and helicopter manufacturers also conduct public flight testing of aircraft and components or fly aircraft in public view to test ranges or other corporate airfields for training or demonstrations. Occasionally, some of these aircraft will be made for military clients and are painted in black or dark colors.