Whenever I try to enrol in a course it says "Available seats are reserved and you do not meet the reserve capacity criteria". This is causing a lot of headaches. I have emailed the different course departments asking to open a spot for me. Anyone else having/had this issue?

Maybe the classes are full because the spots in the said classes are actually reserved for people in relevant programs that must take those courses?

Upper years usually get preference with all courses (they're the first to register). i'm not sure if this still applies but once upon a time when we used mugsi, it would close after the initial registration period was over and when it reopened 2 weeks later, spots were still available once you met the criteria.
Double check you have the prereqs and drop in to see the department if possible. I'd imagine they're all swamped with emails about courses and registration right now.