My guess is that the points are not the same. You are only seeing the points xyz location rounded to three decimal places. Dynamo is looking at the tenth decimal place (may not be the tenth but it is deep). Your points are in slightly different pleases but you do not see it.
I think Point.PruneDuplicates takes this in to account and does not look at the tenth decimal rather the third like you see.
This is an old post of mine between the created or Grasshopper David, and myself. He has explained it much better than I can. You can check out our conversation at the link below. Again this is for grasshopper but I am guessing this is whats happening to you as well.