I completed all the classes and did the final puzzle of the Witch Academy before I did the pyramid quest. Then after doing the pyramid quest the game told me to go to the Witch Academy, but when I went there the game is treating it as if I am starting the Witch Academy all over again so I can't enter the hallways or leave the academy. And because I already did all the classes I can't even register in with the front desk. I do have other save files to get me out of the academy, but I can't continue threw the story until this problem is fixed

I have a similar problem. I did the pyramid quest too early and now the game keeps telling me I need to go there, and I can't progress further.

i got the Sabrina's recommendation but they just won't let me in

Idk what to do

I was also not allowed in and I went to do other quests that were generally possible to do, and then I returned to the Academy and that's it, I'm fine. It's strange somehow!