I think, though I'm not certain, that they still have, 'under the hood,' the old upgrade tree (with many levels of damage increase), and that those are triggering the notifications. So just like the old trees, the non-damage perks were they 3 and 5 out?) actually trigger after a couple of false ones. I'm sure they know about this and are working on correcting it. (In part because this isn't the first post to mention it 😉).
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Still it should have never left the cutting room floor with such an easily found glitch. Bungie need to kick their quality manger in the ass. They keep dropping the ball on such easy fixes.