I have found several references to the square, and nearby Whitefield Square, having been built over a graveyard, including on these websites: gosouthsavannah.com , genteelandbard.com, and ghostcitytours.com. I have copied the passage from gosouthsavannah.com below:
"HISTORY OF CALHOUN SQUARE
Calhoun Square was laid out in 1851, one of the last squares – along with Troup Square to its northeast and Whitefield Square to its immediate east – to be created according to Savannah’s plan.
Calhoun Square, like all Savannah’s Historic District squares, was laid out on the city’s common lands surrounding its already built up areas. The specific area in which Calhoun Square is located, however, is believed to have once been the site of an early 19th century burial ground, where Savannah’s African Americans, slave and free, were buried.
The official location of the burial ground was further to the east, under the present Whitefield Square, but in the absence of any clear markers designating the ground and its boundaries, many people were inevitably buried outside of its limits.
A human skull was unearthed in Calhoun Square in the early 2000s, and it is estimated that several hundred people, mostly slaves, may have been buried here and in the vicinity."