Every time I open the map after launching the game I discover one enclave or another is reporting that I have earned all of the mirabilis, and yet it tells me that 0/0 puzzles are completed. So I wander over that way, do the puzzles yet again, and it sometimes fixes it. Temporarily. Sometimes it does not fix it. The next time I log in... Guess what? 0/0 puzzles completed for that same enclave. I have found this error in the following places thus far:

Verdant Glen: Verdant Glen Quest for Perfection
Lucent Waters: Area Insight
Lucent Waters: Quest for Perfection

Additionally. When you fully complete an enclave or one of those blue diamonds on the map, solving all puzzles for it, I have noticed that it is supposed to place a tan square next to it. If you have not fully completed the area, you receive only a green checkmark. So, here is the problem. Some of those areas that you fully complete are keeping the checkmark and not giving you a tan square.

So far, I have discovered this issue in the following places thus far:

Verdant Glen: Verdant Glen Quest for Perfection
Verdant Glen: Temple of the Infinite Rings
Lucent Waters: Area Insight
Lucent Waters: Quest for Perfection

There are very likely more, but I have not gotten that far yet, as the completionist in me hates leaving puzzles unsolved.