I think its a ggplot issue
You are assigning "name" to shape, but ggplot provides just 6 shapes by default and you have far more names. You can probably force it to add shapes but it doesnt really make any sense. First try plotting it without setting "shape" aesthetic at all - you should see all the points. If you deeply care about identifying points by name , you can add name as a label ( dont forgot to add geom_text() . and I would shorten the names first).
If you want to see how replicates cluster, add another variable to your original dataframe and use that.