Many unidentified remains were interred. It may include remains from both sides.
From the official website of the Arlington National Cemetary:
http://www.arlingtoncemetery.org/historical_information/arlington_house.html The property was confiscated by the federal government when property taxes levied against Arlington estate were not paid in person by Mrs. Lee. The property was offered for public sale Jan. 11, 1864, and was purchased by a tax commissioner for "government use, for war, military, charitable and educational purposes."
Arlington National Cemetery was established by Brig. Gen. Montgomery C. Meigs, who commanded the garrison at Arlington House, appropriated the grounds June 15, 1864, for use as a military cemetery. His intention was to render the house uninhabitable should the Lee family ever attempt to return. A stone and masonry burial vault in the rose garden, 20 feet wide and 10 feet deep, and containing the remains of 1,800 Bull Run casualties, was among the first monuments to Union dead erected under Meigs' orders. Meigs himself was later buried within 100 yards of Arlington House with his wife, father and son; the final statement to his original order.
The federal government dedicated a model community for freed slaves, Freedman's Village, near the current Memorial Amphitheater, on Dec. 4, 1863. More than 1,100 freed slaves were given land by the government, where they farmed and lived during and after the Civil War.
Neither Robert E. Lee, nor his wife, as title holder, ever attempted to publicly recover control of Arlington House. They were buried at Washington University (later renamed Washington and Lee University) where Lee had served as president. The couple never returned to the home George Washington Parke Custis had built and treasured. After Gen. Lee's death in 1870, George Washington Custis Lee brought an action for ejectment in the Circuit Court of Alexandria (today Arlington) County, Va. Custis Lee, as eldest son of Gen. and Mrs. Lee, claimed that the land had been illegally confiscated and that, according to his grandfather's will, he was the legal owner. In December 1882, the U.S. Supreme Court, in a 5-4 decision, returned the property to Custis Lee, stating that it had been confiscated without due process
On March 3, 1883, the Congress purchased the property from Lee for $150,000. It became a military reservation, and Freedman's Village, but not the graves, was removed.