I'd like to know how you treat your cells in culture after sorting them. Do you use any extra antibiotics to avoid contamination? What should I do in order to be as sterile as possible?
Depending on the type of cell sorter and the conditions of use and maintenance you may be abl to preserve sterility. In any case, it is a good idea to add gentamicin as Diana suggested, during a few days (3-4 media hanges or 2 passages). Most cells tolerate well gentamicin.
Another suggestion is to have more serum in the medium where the sorted cells fall and avoid centrifugation for 15-30 min after sorting.