paper trees don't count for a bunch of things (all the various badges, later quests to tend each type of tree).
given they're in like 5 or 6 locations now rather than the original one maybe they should.
other wise maybe an info box proclaiming that "you found a paper tree!" explaining that they are special trees might be warranted the first time you interact with one (or see one). I might go so far as to make it an early tutorial quest to find one and really nail it home that they're different.