You want to show two different points at different locations on the x axis. But currently you have them with the same values for x.
The answer is simple. You need to adjust the x coordinates the duplicate points will be plotted at. Yes, I know that you want MATLAB to know what you want it to do. But it cannot read your mind, and if MATLAB decided to plot points at locations other than where they were specified, then I am sure someone would start to scream about a bug, accompanied by a great deal of wailing and gnashing of teeth.
But you do not need this by hand. Simply search for duplicate points. You can use tools like diff and find to identify exact duplicates, although you may want to use a tolerance to identify them. Then just add and subtract some small number from each x value. Again, that is easily automated.