In addition to the effect of the water (which I don't understand - see below), there are other things that can cause you to calculate negative FS. If you have are doing a limit-equilibrium analysis that involves shearing through concrete in the upper part of the slope, some programs can produce negative interslice forces so large that FS can actually get negative. You might also see this happen if the exit is much steeper than 45-phi/2, which can cause spurious negative base force. Go through all of your base forces and interslice forces looking for weird ones.
I'm puzzled as to how the water pressure can exceed the weight of the slice, assuming you are putting the TOTAL unit weight in for the soil.
Can you post a sketch?