This question already has an answer here:
Another Minhag that came from nowhere is the custom of filling a wine cup to overflowing. Some do it because of Kos Pagum, however it seems that Kos Pagum applies to a cup which is not filled near enough to the top to be considered full. Overflowing the cup is ba’al tashchis as well as davar m’geunah. Getting wine all over your hands and the tablecloth is not good table manners especially if you are a guest in someone else’s home. The only time there appears to be a reason to do so is havdalah when it is considered a berachah. Is there a source for this?