Why would there be unmarked graves in a National (i.e., American military) Cemetery?

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The use of stone blocks for marking unknown graves in national cemeteries was discontinued on Oct. 21, 1903, and the graves were marked with the same design as those furnished for the known dead.

In order to ensure that all graves in military controlled cemeteries were marked appropriately, Congress on April 28, 1904 (58th Cong., Chap. 1762), also authorized the furnishing of headstones for the unmarked graves of civilians buried in post cemeteries.

http://www.cem.va.gov/history/hmhist.asp Even at Arlington there is sloppiness approaching scandal in record keeping which is slowly getting caught up with but is far from perfect. The work continues to improve as inadequacies are discovered, stemming back to the Civil War.