Sometimes the same co-ordinates are shared by more than one observation. A scatterplot will only, however, show one point for each unique x,y combination regardless of the number of observations that share this combination.
One way of disentangling this is to add a proportionately small amount to the observed values of one of the variables, say, y. The below syntax uses the rv.uniform function in SPSS to add a small random amount to the y values. The new values which are now all unique (ynew) can then be plotted against x.
COMPUTE YNEW = Y + RV.UNIFORM(Y*0.01,Y*0.015). EXE.