When you get an equipment of a higher level, this takes the place of a lower level one. Thus the rare equipment got applied, and the uncommon one became Enhancement Points (2, because it's uncommon). Pieces of equipment don't get multiplied, only the rarest in any given slot is equipped.

yes, a berry is different then something else like a hardwood, and yet something else like an amber. and each come in varieties from common to uncommon, to rare and epic (and with possibly golden epic at some future date) and possibly something called legendary which we have seen in someones posted image (possibly hacked but not photoshopped).
enchanted points is like 1x, 2x, 3x and 4x depending on what was duplicate.
p.s. you can press P in game and see the play history which might describe in more detail what you got and what happened to it. but do that within a day or so as the history is limited.