Edit: Got the answer, apparently my mistake was to think you could get the points more than once per day. 😐
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So I just did my weekly evolving of my Megas to earn more points. As far as I know it should add 6 points per evolve. And it did, with most of my Pokemon, I could max out some which otherwise still had several evolves to go.
But then I noticed that Kyogre and Groudon only got 1 point. Okay, technically they are Primals, but seriously? Okay, maybe an oversight from Niantic, maybe intentional, whatever.
But then I wanted to level up some more Pokemon which I have plenty of mega energy for. But right the first one didn't get any more points at all. As I wanted to remove 12 from the 14 points left from my Latios immediately after evolving I noticed it still had 14 to go, I even evolved it once more to be completely sure and make screenshots.
So here we go, the pictures show it had 14 left to do, I mega evolved it, it still had 14 left.
Is this a known bug or what is the reason behind this?
Edit: Made a mistake with adding the pictures, so here they are: https://imgur.com/a/lpI4Gkl
by real_fyshi