I am getting the same issue too.
My character has the level 3 Path of Ascension upgrade, “Continued Training”, unlocked. However, it seems like the upgrade effects from level 2 and level 3 of that upgrade are not unlocking correctly.
The level 2 Path of Ascension upgrade, “Sacred Trials”, is suppose to do a few things. First, allow the capture of 4 more memories, which should increase the total number to 10 (which is how many bosses there are in total). And second, empower some of the memories to unlock their level 2 encounters. Neither of these are occurring. The last thing it is suppose to do, was unlock a weekly quest, which, it did.
The level 3 Path of Ascension upgrade, “Continued Training”, is suppose to unlock the remaining level 2 encounters for all bosses, and one of the level 3 encounter. Neither of these occurred. It is also suppose to unlock the ‘Brazier of Lessons Learned’ in the game mechanic, which it did.
I did notice something odd, the level 5 upgrade reward, Inward Reflection, was active in the POA game mechanic, when it shouldn’t be, since I do not have that upgrade.
As for the bosses, I have Kalisthene, Echthra, Alderyn & Myn’ir, Nuuminuuru, Craven Corinth, and Splinterback Nightmare unlock. And these bosses only have their level 1 encounters unlocked. I have also completed all their level 1 encounters, and receive their rewards. Fighting the level 1 encounter again, just rewards random crafting resources.