The S phase is the period where DNA replication takes place. It is possibly because, at the time of harvest, most cells were still in the active cell division phase. To further confirm it, repeat the experiment by harvesting the cells at different time points and check the cell cycle analysis. You can also isolate peripheral blood mononuclear cell (PBMC) and read the cell cycle analysis. If the unusual high content of S-phase continues, you may check three other possibilities:

1. Cells were not stained uniformly and incomplete mixing
2. Cells were gated improperly
3. Cells were non-specifically stained