The current theory suggests the US secretly supported the Islamic State so the Islamists would destabilize the government of Syrian President Assad. If that seems out of the question, remember the CIA once started a war over bananas… literal bananas.

Cuba: Probably the best known secret army. Castro nationalized the assets of western companies after his government took power,  so the US decided to overthrow the government of Cuba and install a puppet regime. As with most of the armies backed by the US intelligence establishment, it failed. Miserably. The Bay of Pigs invasion saw 1400 US-trained Cubans surrender to Castro's forces within 24 hours.

El Salvador: The US-supported Salvadoran government faced opposition from communist rebels. US intelligence saw an obvious and simple answer: establish death squads. US intelligence trained and advised pro-government forces as they massacred villages and led the way to the displacement of over a million people. Immediately after the ceasefire, there was a general amnesty for people implicated in war crimes.