have you checked, before doing transfection, if your cells adhere properly?
It happens to me with HEK293T when I seeded them on coverslips or whatever different from canonic plates that I had a lot of cell death, making difficult to perform experiments.
Hi, we use 1-2ug of DNA (vector) with 5ul of lipofectamine for HEK293T cells in a 6-well plate (1,5x105 cells/well). We also add the solution drop by drop to avoid problems with the adherence.