The states of New Jersey, Delaware, Maryland, Missouri, West Virginia and Kentucky all continued practicing slavery throughout the war.  These same states sent Union regiments to fight confederate soldiers, most of whom never owned any slaves. 

 Is it possible that federal troops from the north invaded their neighbors to the south, to end slavery, while it was still legal and thriving in their own states?    

Delaware, Kentucky and New Jersey initially refused to ratify the 13th Amendment to formally abolish slavery after the war. Delaware did not ratify until 1901.